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Digi Doc-It User Manual

1. Image Windows Status Bar Related Topics AA amem Menu sus ime 0 ea Aoa Ua Toolbars Especur Tira Linn Hes EAD 3 et Lord C7 Light Source Ts 5 NES DAA Color bf znanc Tate E ur Earache Sint Ero z O PRR DIU PROS es RO O OO 000 T5 ol Lok Capa J F Deer rake Eein Ari f Lead mio Cuan iaga indo Capture Panel AA E E RT EE WA IMA Pee M87 Had 8 Cavan A status Bar Image Window The Doc It Main Window contains the application s menu bar toolbars image windows Capture Panel and status bar as indicated in the diagram above Some parts of the window such as the toolbars Capture Panel and status bar can be hidden or shown as you prefer To Show or Hide the Toolbar On the View Menu choose View Toolbars All of the individual toolbars and the space they occupy just below the menus will be hidden or shown 11 Doc IT USER MANUAL To Show or Hide the Status Bar On the View Menu choose View Status Bar The status bar will be hidden or shown To Show or Hide the Capture Panel On the View Menu choose View Capture Panel The Capture Panel will be hidden or shown When the Capture Panel is hidden you cannot control the camera or change the Effects settings MENUS Doc It offers the following menus F Digi Doc It File Edit View Acquire Image Tools Formatting Window Help Although most commands appear on the menus some Doc It features are only ava
2. Related Topics OVERVIEW Annotations allow you to mark areas of an image without changing the image itself This means that you can indicate areas that need more study that are particularly interesting or that support a particular scientific interpretation When using annotations imagine that you have a transparency over your image on which you can write or draw At any time you can remove or replace the annotation layer to see the image with or without annotations Gel with Annotations 60 Doc IT USER MANUAL The next seven topics explain the annotation system in more detail e Creating Annotations Explains how to create annotations e Deleting Annotations Explains how to remove annotations you no longer want e Formatting Annotations Explains how to use the Formatting menu when creating or editing annotations e Moving and Resizing Annotations Explains how to move and resize annotations graphically e Selecting Annotations Explains how to select annotations e The Text Edit Window Explains how to use the Text Edit window for entering and editing text annotations e Types of Annotations Explains the annotation tools provided in Doc lt e Viewing and Hiding Annotations Explains how to show or to hide all annotations on an image VIEWING AND HIDING ANNOTATIONS Although annotations are useful for drawing attention to important features sometimes they cover up features you need to see You can view or
3. Related topics OVERVIEW Molecules in an electric field migrate through a gel matrix at rates inversely proportional to the log10 of the number of base pairs Large molecules migrate more slowly due to large frictional force from the pore of the matrix while small molecules migrate faster due to less frictional force There are many experimental conditions affecting the migration rate gel concentration conformation of the DNA applied voltage direction of electric field base composition and temperature presence of intercalating dyes and electrophoresis buffer It is therefore desirable to use a known molecular weight standard as a reference to unknown samples This marker is used to calibrate the resulting molecular weight for each unknown bands Using a molecular weight marker results in a band encompassing the whole gel horizontally This band can be thought of as the distance traveled of a band relative to its front Retardation factor Rf or starting position This Rf line exists for each band in the molecular weight standard Any bands in the unknown samples that migrate to any of these Rf lines are then compared to the Rf lines In this section you will learn how to manage molecular weight standards and calibrate lanes to these standards This section also explains how to determine Rf values automatically how to add Rf lines manually and how to move and delete Rf lines In general Rf line functions are only required if you ha
4. e IRE SEO 5 erat cine ae seen es dew I I ee E 11 FOO lo 10 AA A o PP O 11 ISO as 39 ISO ito 85 HOW sie T TTE MT T 127 Doc IT USER MANUAL Computer Images Work iii A AA 42 A ce T Mage a a e S 18 A a dees TET 18 DEPI MP Oo TD PH S 122 IS LOL A A II iot De A A A 70 MONO MN RE MET TTA 68 EG AGING AAA A A A dT ICE I 29 EN Po UP DE 30 A 2 Re ae a nr a uu dud ud eer ee eee 38 A re ea er kit EI C ee eee eee dass 123 A E m 18 LOOF Ces letus poen M ML uu M I i ie bed di ie M MM 18 Iwrleiwiw zeeemet d M 122 image Background Colas A ii 85 Mage FIG SI A la ad 122 Image Informatiecentra aia 68 80 85 HISTON de HT 70 Image Information WINdO Wisin i n 80 Mage Miu RUE 12 Mage VV ING OW mL ies 18 Mage Window FS ate T AAA AAA A A 83 Is Te Daa EXI ana RET 111 Heude Band Total aia da 111 o A PP eer et et se E ee TT T Nal Tolpar BUON RETE TETUER 82 INSIST UX ON Pret PT e e a as 42 A N sed seen tes aee sea cease a sce 106 109 113 118 122 mienne x e L 39 SVENN eee 40 MERSI ISO EORUM acodi 39 A HH UU CE 40 J Jis nico Valle yS c cee 85 99 JPEG densa ien oso chum a patur ae eo ioo dae Studie 31 122 K Key Management sen mts dutvo Dude dinde unde O a 4 L bane CUVE EINGS ete RUP ET 80 BABA O q e octies EU eu itai ee en ee eee a i UE 111 A O A A Mu uu ex 80 85 106 113 118 Ez qM 80 85 11
5. 1 From the 1D Analysis menu select Edit 1D Objects 2 Select the Rf line to delete 3 From the 1D Analysis menu select Retardation factor Rf Lines and then Remove Rf Line pi You can also delete a Rf line by selecting it and pressing the DELETE key To Remove All Rf Lines 1 From the 1D Analysis Menu select Retardation factor Rf Lines and then Remove All Rf Lines pi You also can access these features using the 1D toolbar MOLECULAR WEIGHT CALIBRATION Managing Weight Standards Calibration of molecular weight involves associating a known standard with one of more lanes in the image This allows Rf values to be calibrated to molecular weight values Doc lt allows you to use several different standards per gel 94 Doc IT USER MANUAL To help you in your analysis Doc It keeps a library of molecular weight standards You can add edit and delete standards from the library using the following instructions ES RUIT 00 E Xl Adding a Molecular Weight miam arte abr Standard to the Library 1 Select the Lane to calibrate and click on it 2 Under the ID Analysis Menu select Lanes and then select Calibrate Molecular Weight A new window appears In the new window click on Add Another window appears In this window first select the Group name Then type in the name of the standard which you are using In the third line select the Unit Type Click Add This allows you to enter the numerical
6. 1 Unplug any other parallel port devices from the computer s parallel port 2 Attach the security key to the parallel port 3 If you have other devices such as a printer you can reconnect them to the other side of the key How To START THE APPLICATION 1 From the Windows Start menu click Doc It KEY MANAGEMENT The Key Management feature allows UVP to manage user permissions for the application remotely Currently Doc It has two features that require HASP key permissions e The Camera permission allows you to use the camera and hood hardware A HASP key with this permission is provided with the hardware itself from UVP e The 1D Gel Analysis permission allows you to use the 1D Gel Analysis menu and features As Doc It initializes it will read and configure the program as required to enable access to permission protected features Doc It will keep checking for the presence of the HASP key as the user tries to use protected features This means that you can see what permission the HASP key provides you and it allows UVP to upgrade permissions remotely To Find Your Key Number Each HASP key has a unique number You can see your key number by loading the About window select About from the Help menu and looking at the bottom left corner The key number will show up beside the Key label If it reads Key O there is no key installed UVP will need this number to provide you with additional permissions Once the Key
7. O The zoom factor matches the values on the Effects tab A zoom factor of 100 means that pixels in the image are being shown in actual size This may mean that the entire image cannot be displayed in the Image window depending on the size of the image and on your video mode settings Changing the zoom factor of an image does not damage it in any way Showing the Image in Actual Size To show the image in actual size no scaling choose Actual Size from the View menu You can also use the Effects tab to set the zoom factor to 100 Fitting the Image to the Window To show the entire image in the window scaled up or down as required to make it fit choose Fit to Window from the View menu Context Menu Commands A context menu is a menu that appears when you click on the image itself with the right button of the mouse Itis a shortcut menu that lets you sidestep using the menus or the toolbars Once you bring it up treat it as a regular menu by selecting features from the list By clicking on the image with the right mouse button in Doc It a menu with the following 19 Doc IT USER MANUAL commands pops up e Copy e Paste e Paste Special e Actual Size e Fit to Window e Zoom e View Annotations e Image Information e Intensity Histogram pi Both the Actual Size and Fit to Window commands are also available from a shortcut menu on the Image window itself The shortcut menu can be displayed by right clicking on the image
8. STATUS BAR The Status Bar shows the current mouse position in an image the intensity of the image at that position and status messages during long operations Pos 159 1 ribera FSX 47200 951 FH The mouse position is displayed in pixels X and Y The intensity is displayed as a single value if the image is monochrome and as three values Red Green and Blue if the image is colored In both cases the value is reported as a percentage value of the maximum intensity Related Topics Chapter 2 Using Online Help Chapter 4 Basic Capture Tab Chapter 4 Advanced Capture Tab Chapter 5 Loading Images Chapter 6 Editing Chapter 7 Special Features Chapter 8 Effects Tab Chapter 9 Manipulations Chapter 10 Annotations Chapter 11 Image Information Chapter 12 Printing Chapter 13 Customizing Doc lt 20 Doc IT USER MANUAL CHAPTER FOUR ACQUIRING AND MANAGING IMAGES Overview Olympus Camera o Basic Capture o Advanced Capture o Camera Settings o Capture Templates Scanning Images Related Topics OVERVIEW Doc It allows you to acquire images in three ways e You can capture images from the supplied camera e You can scan images from most scanners e You can load images from disk This allows you to return to images saved during a prior session and to import images either produced through some other software package or transported from a Doc It installation on another computer Loading and saving are discu
9. This will help you to drag the grid in the right direction and to avoid flipping the image 180 degrees by mistake Once the appropriate grid line is aligned with the feature click OK on the Rotate window Aligning a large image can take fifteen seconds or more from the time you click OK To Rotate an Image to a Desired Orientation If you have a desired orientation for the image you can use the Rotate mode of the Rotate manipulation From the Image menu choose Manipulation and then Rotate The Rotate window will appear and a grid will be overlaid on the image cun If the image has not yet been saved you will be prompted one time to save it before the first manipulation you select 2 On the Rotate window select Rotate 3 Drag the grid so the yellow arrow moves in the manner you would like the image rotated 4 Once the grid is oriented to your satisfaction click OK on the Rotate window Rotating a large image can take fifteen seconds or more from the time you click To Rotate an Image by an Exact Number of Degrees You can also rotate the image by an exact number of degrees For example you can correct for an upside down gel through rotating by 180 degrees 1 From the Image menu choose Manipulation and then Rotate The Rotate window will appear and a grid will be overlaid on the image For this operation you will ignore the grid mo If the image has not yet been saved you will be prompted one time to save i
10. You can hide the Capture Panel to make more room for your images From the View menu choose View Capture Panel to hide or show the Capture Panel It s also on the toolbar IMAGE WINDOWS Each image that you generate or open in Doc It will appear in a separate Image window You can have several Image windows open at one time z Cobre doom 15 18 Doc IT USER MANUAL Organizing Image Windows e To bring an Image window to the forefront either click on the window s title bar or find and select the image s filename from the list in the Windows menu e To move an Image window drag the window s caption in the normal manner e To resize an Image window drag the lower right corner or an edge to the desired size e To tile all open Image windows choose Tile Horizontal or Tile Vertical from the Windows menu e To cascade all open Image windows stack them so that all the captions are visible like an index card file choose Cascade from the Windows menu pi If you find that you frequently work with multiple images at one time you may want to put the Windows menu commands described above on the toolbar by customizing it Information Provided by the Image Window Besides just displaying an image the Image window tells you e The filename of the image e The current zoom factor of the image Both pieces of information appear in the Image window s caption ro A caption of Untitled means the image has not yet been saved
11. points Doc It will fit a curve to the points using the method selected above the graph plotting this on the graph Editing Data Points To edit the data points that you already selected Deleting Data Points To delete data points from the graph 1 Click on the Data Points tab of the Calibrate Intensity Window 2 Click on the value that you wish to delete 3 Click Delete 4 Click OK 103 Doc IT USER MANUAL SELECTING CURVE TYPE Once you select the data points to graph Doc It allows you to select the type of curve or line to fit to the data points 1 To select the line or curve type in the Graph tab of the Calibrate Intensity Window to the right of the graph find the Curve Model option Select the type of curve you would like to see on the graph Doc It has six possibilities for Curve Models e Least Squares Line a straight line polynomial degree 1 e Least Squares Quadratic a binomial curve polynomial degree 2 e Polynomial 3rd degree a polynomial curve of degree 3 e Polynomial 4th degree a polynomial curve of degree 4 e Bezier Bezier curve algorithm and e BSpline B Spline curve algorithm In using polynomial curve types make sure that you have at least one more data point selected than the degree of the curve e g if you select a Polynomial 3rd degree you need at least four data points To use the Bezier and B Spline curves you need at least three data points Doc It automatic
12. 46 ALOT NUT pats 10 SR See ee nee tolit asd cesi M E hl d DI MIC MO E uds nir NM Ed M DEG 47 ziie eegei r e 122 EITIDOSS auct suc t a ac ario lali 56 DEA A ici RI LMELLDDI RIETI DM Ee LM UD AIL el LIOK LAS a Er 8 cans 96 a 4 61 0 4 gt m eT EP 18 SHOWING Or PICMG saca o mot 11 A ELLE 18 EXPO DUO o e a e e a at A d ano 113 EDAD A O E 114 F meii RR T mm T mie eR CE En 122 File Format BNIE cum i EA CE E EL Ea 31 122 Ip teu out t bed MM e mU teal D 31 122 Mmi ta EET 31 122 mica mE ES 31 123 jer EUR METER 31 123 TIE ouis a med hat Ecc Ma t a ec Sm Mone Nim snif SC LUE 31 123 gii ucmeb MU T Umm 113 114 minis UN TRE S 87 EID bates and Bands arde 80 82 Flip FIOLIZONLAMY eT AAA o4 NW GILICAINY EE o4 PONE SIZE Bard uio as comes acelera dise a a ti ace LEO 85 PORE elu ig RTT 85 FOOTE TO a 115 117 118 119 120 Formaning AANOTAU OMS iaa id A add A dia 66 A ON MMA CU ETC Mena 12 o een treet ENORMI 102 G A M M 31 122 GO0ANEsSSs Ol TT 104 O 104 Graph USINO Gol T EE M 120 H plato pal lt Sst E TU UI ER 4 Header Tecna oido Loto LL LM MO eones 115 117 118 119 120 POND e EMI pcm T EE E cbr E teeter E E E A E O A eee A T ee eee 12 A a a T a O 11 AMOO Sara o ti a nada oo a dcir dla CENT 61 EXI ri co ias 11 A trac eset TE 38 RS CMU cl
13. 94 APPplING a Standard to a Cahe seniore 96 Calibrating a Lane aa O A 96 Using the Stretch Facil el 97 Removing a Standard from a Lane c oocnccoccccccncocncconncncnnnanononnnnanonnnnnnnncnnnonanonaninnanoss 98 CHAPTER SIXTEEN USING THE 1D GEL TOOLS FOR CONCENTRATION CALCULATIONS 99 Gu TC C 99 ire e qou aoEGredicledlo a RETE m tt 99 Background Correcob ODEUOPS ua cse tooo 99 Viewing a Corrected Image ooccccccccccccnccccnnccocnnnconnnononononannnonnnnonnnnnnnnnnnnonnnnnannnonananenannnnanos 101 Cohcentradon CallbEAllOD usse eve a dida 101 Showing the Concentration Graph sssssssssssssssseseeeeee nennen nennen nnn nnn 101 Selecting Data POIDS temita 102 SGlCCIING Data PONS V M 103 Editino B 1s POMS Tm 103 Deleting Data Polti aded oceania tae cep Pado pedido n aires tp ade 103 Selecting CUNVE TP n EN 104 Removing Concentration Calibration oocccccccccncccnicocnconnnonnncnanocncnnonnnnnnnnnnncnons 105 CHAPTER SEVENTEEN VIEWING AND PRINTING 1D GEL DATA eene nennen 106 VT VIC Wa iat naa 106 Cane Into Mal at 106 To View and Use Lane Properties x t ei eae eee ees 106 A 107 To View and Use Band Properties eese nennen nennen nnn nnns 107 Lane PONE Grap E o 108 Displaying Multiple Lane Sassena a 108 AXIS ODIO times tata 109 Display ODION S er at
14. An open Universal Serial Bus USB connection e A parallel port connection e Color monitor 16 bit color 32 bit color or greater recommended e 1024 x 768 or greater monitor resolution NOTE Prior to installing a INSTALLATION INSTRUCTIONS new version of the software uninstall any previously installed e Install the Doc It Software Doc It software If e Setup the camera hardware upgrading and already have a security key connect the new key to the existing key on E a your PC Installing Doc It requires several steps each of which are detailed below Doc IT USER MANUAL INSTALLATION INSTRUCTIONS Installing Doc It requires several steps each of which are detailed below e Install the Doc It Software e Setup the camera hardware e With the computer off connect the camera to the computer and turn the camera on e Install the camera driver software e Insert the camera into the hood Installing the Doc It Software 1 Insert the CD into the CD ROM drive The installation program should start automatically If the installation program fails to start navigate to your CD ROM drive and double click Setup EXE to launch it 2 Follow instructions from the Wizard screens as they appear clicking Next Accept or Finish as appropriate 3 If prompted to restart your system click No 4 When the installation has finished click Shut Down on the Windows Start menu to shut your system down To Set Up the Camera Hardwar
15. Contrast Gamma Or Invert 1 If the image is not the foremost image select it from the Windows menu or click on its title bar 2 Ifthe Capture Panel is not showing or is showing a tab other than the Effects tab choose Effects from the Image menu pi You can also show the Effects tab from the toolbar 45 Doc IT USER MANUAL 3 Tochange Brightness slide the Brightness control either left or right or type a desired brightness value into the Brightness text box to the right of the slider 4 Tochange Contrast slide the Contrast control either left or right or type a desired contrast value into the Contrast text box to the right of the slider 5 Tochange Gamma Contrast slide the Gamma control either left or right or type a desired Gamma Contrast value into the Gamma text box to the right of the slider 6 To invert the image select the Invert check box T To stop inverting the image clear the Invert check box To Return to Default Values 1 If the image is not the foremost image select it from the Windows menu or click on its title bar 2 If the Capture Panel is not showing or is showing a tab other than the Effects tab choose Effects from the Image menu 3 Click Reset PSEUDOCOLOR This applies a false color spectrum to a monochrome or colored image This process is sometimes called colorizing There are two primary reasons for using pseudocolor 1 To make the image look more like what might
16. E a Be prs m que Y OF ay EF EF mr pra E Y PRESSE es e To Change General Layout Before Printing 1 To change the title of the report as it appears on the printout type the new name at the top 2 To change the margin size click on the drop down menu under Margins You can make the margins larger or smaller by varying degrees To view the margin lines select Draw Margin Lines 3 To change what appears in the Header Text or Footer Text note the following abbreviations for header and footer text op puts the page number at the top or bottom of the page Joc puts the page count at the top or bottom of the page d puts the date at the top or bottom of the page and Jot puts the time at the top or bottom of the page Click Refresh Preview near the top left of the window to effect the changes pi You also can access this feature using the 1D toolbar Analysis Lanes Doc It will print a fixed report of the lane analyses for you In this report you will find the following information 118 Doc IT USER MANUAL e The Lane ID and name e Where the lane starts and ends e he band count e The mass of the lane e The unit of mass e The intensity maximum e The intensity volume e Molecular weight information e The concentration maximum and e The concentration volume To Print the Analysis Lanes Fixed Report 1 Under the File Menu select Reports and then select Analysis Lanes A preview wind
17. Effects tab and set Pseudocolor to None Decide if you would like to reuse one Image window for all images or to generate a new Image window per capture If you would like to use a single Image window select the Load into Current Image Window check box if not clear the check box 5 Click Capture Advanced Capture Tab The Advanced Capture tab is one of three tabs that make up the Capture for pon lp er 7 Panel It is designed to give you full control over all features of the Olympus Ses camera iii The tab consists of three parts eared eat ett e The Template drop down list which allows you to select a pre built cm or capture template Doc It comes with some standard templates for AE T use with various light sources You can also select Photo which i T gives you direct control over the camera using the camera default da m settings ee e The settings control area in which a variable number of settings will rca Sahat Fg appear depending on the Template you select For Photo all pale settings are available All settings also will be available if the selected template does not exclude them Otherwise some n settings may be suppressed for simplicity e The Capture and Templates buttons These buttons appear for all templates near the bottom of the tab A dde rad Lcd b mis Templates are a great way to set up groups of camera settings that you use frequently For more information see Working with C
18. Lane Profile Graph e Inthe Data Explorer e In Tabular Reports e In Analysis Settings and e In Band Properties This section covers Band Properties To View and Use Band Properties 1 From the 1D Analysis Menu select Bands and then select Band Properties A new window appears 107 Doc IT USER MANUAL AA Inlormalnin i In this window Doc It allows you to Bored ID ee N me perform two changes to the band e You can name the band and Geometry aaa E e You can change the geometric T 2 Peak E Bolton 2 m proportions of the band L alculared Peak Values Fi Value 033 Molecular weigh H Band Properties also offers you the following information kens The Band ID arum o 4353 83 The calculated peak values Rf value and molecular weight Concentration The intensity of the band HUI NM ENIM pai including its maximum volume AA N HA JA s i i percentage of the lane and C mass and The concentration of the band including its maximum volume percentage of the lane and mass pi You also can access this feature using the 1D toolbar LANE PROFILE GRAPH Doc lt allows you to view profile graphs intensity vs position of one or more of the lanes in your image in the Lane Profile Graph To access this function select Lane Profile Graph from the 1D Analysis Menu A new window appears with the graph itself and with several options Underneath the gr
19. M Umi cd pr pz AW pg I Lom cdit Fut pg a Urna 5g A AP p E Eha pz A mmus F M irere To Save a New Image 1 From the File menu choose Save The Save window will appear pi You can also use the Save button on the Toolbar 2 Selectthe file type that you would like to use from the drop down list near the bottom of the window 3 Navigate through the drive and folder structure to the location where you would like to save the image 4 Enter a filename for the image 9 Click Save To Save Changes to an Image 1 From the File menu choose Save or use the Save button on the Toolbar Changes will be saved to the existing file overwriting the previous image data To Save Using a Different File Folder Name or Type 1 From the File menu choose Save As The Save window will appear 2 Select the file type that you would like to use from the drop down list near the bottom of the window 3 Navigate through the drive and folder structure to the location where you would like to save the image 4 Enter a filename for the image 5 Click Save 30 Doc IT USER MANUAL IMAGE FILES Images in Doc lt are saved as two separate files While the two files have the same name and appear in the same file folder they have different extensions The Image File The more important of the two files is the Image File as it contains the actual image lt is saved in the image file format file type selected when saving which
20. RA T lo g Mer 106 107 109 Molecular Weight Calibrates ccoooococcccononcccocnncccoononcnnonoconannnnononnonnnnannnnononnnnnnnnnnnnnnannnnnnnns 82 Molecular Weight Standard zs ua iia 94 Molecular Weights Standards liSt ooooccccococnncccconoconoconnnconnnnonnnnononnannnnonannnonnnnnnnnnannnnnnonas 98 ODIO MIRON SN RETE N 123 Reducing Color Image T0 do nadie gus 58 MOVE BANO sea Sites era t hi pa SUL M pL Ui EET M Ea A pL ict 89 MOVIN O Lastra do oro oca ia 94 MOMO TIO CATIONS racional dee 65 KAUNID Ez a S eean TNR TREE HEN ECT ELDER 108 ISI IS reo rado lr ener pinu dd 108 MA A A icta tdi tetuer te teh oce 75 N Noise PernOdiC NOISE fsermioVal uie ipe od tidad 55 NoiSe Removal sortdan a a a A T senate 55 O VV a SC Sel dcus ccntum T acne eee eee MI me R 21 Bei y PEE ert nee ie oe nee nee ne ea I ae O 76 P x me o nn Ma 35 into Other Software Packages ende ia 34 Paste Special T 35 Slgiere greMes PER 32 129 Doc IT USER MANUAL Periodic Noise ROMOV A EET 55 mic RETIRER 123 Understand uscar EER 42 PIN O uds esi E M AMICO E 31 123 F OMV MOMs SIC EP Tr 104 A A tun MEE ela UT She Ru LA EDAD iba 104 ARCS IAS A ORR eM RARE A ENIM TOA EME CREM MIR ad IUD NOM 82 O TEE LET PEERS 84 Preferences WIN Winnie haa baad not 80 PMA o a a cate CREME E LEM t taco la deat atte 111 119 120 Poni eA EMA REPON eek trios 115 lA E reo arene etre PME 14 PSCC OC OlON
21. REDUCE TO MONO This manipulation reduces a color image to monochrome This is primarily useful when colors in 58 Doc IT USER MANUAL an image are distracting rather than informative For example if light strikes certain surfaces from some angles a rainbow effect prism will appear Another use is to adapt for some software packages and techniques that require monochrome images or which are less reliable on color Images In Doc It the Reduce To Mono manipulation uses a weighted mix of colors to arrive at each pixel s monochrome intensity Green is very heavily weighted while blue is almost disregarded To Reduce a Color Image to Monochrome 1 If the image is not the foremost image select it from the Windows menu or click its title bar 2 From the Image menu choose Manipulation and then Reduce To Mono Reducing a large image to monochrome may take a few seconds If the image has not yet been saved you will be prompted one time to save it t before the first manipulation you select Related Topics Chapter 3 Image Windows Chapter 5 Saving Images Chapter 6 Undo Chapter 6 Using Selection Tools Chapter 6 Copy Chapter 11 Image History 59 Doc IT USER MANUAL CHAPTER TEN ANNOTATIONS Overview Viewing and Hiding Annotations Types of Annotation Creating Annotations Selecting Annotations Moving and Resizing Annotations Editing Text Annotations Formatting Annotations Deleting Annotations
22. a A bode neni neue bates Poaceae 110 Ha e e E LH 110 Background Correction Options cccccoccccccoconcccocnonoconnnnnnnncnnnonannnononnnnnnonnnnnnnannnnonannnnnnonaness 111 Data Explorer and Tabular Reports oocooccocccoccoccconcoccconconoconcnnconononoononanonnnononanonos 111 Managing Tabular Layouts cai 111 Viewing Data in the EXplorer ioi obo tas ccee dala Se UE I eec Dorada Eie conta pd a aa quoc 113 mii IAG Data iaa aan 114 VI Doc IT USER MANUAL Tapular REDO Sui ta 115 TOPi Tabular IED OMS tematica il lei canilla 115 EXPO Data asas 116 EN A alc oT A AN 117 1D EXET REPOS aene a EE T asst EET 117 Analysis SONNO cm ERR 117 Analysis a E 118 AnaS Band Seear N A 119 Lane rone REDO E A E UE O EEE oo tenes ed eU eae weenie 120 GLOSSAR aa o a 122 INDEX A E 124 VII Doc IT USER MANUAL END USER LICENSE AGREEMENT License Agreement Please read the following license agreement carefully END USER LICENSE AGREEMENT PLEASE READ THE LICENSE CAREFULLY BEFORE USING THE SOFTWARE By using the software you are agreeing to be bound by all terms of this License If you do not agree to the terms of the License promptly return the uninstalled software and its complete packaging for a full refund to UVP Inc 2066 West 11 Street Upland California 91786 If you do not agree to the terms of the license you are not authorized to use or keep the software LICENSE In consideration of payment of the License fee
23. allow you to compare several images e Capture button Triggers the camera s shutter and displays the resulting image The Exposure Time setting offers an Auto selection If the Exposure Time is set to Auto the camera will attempt to set the best exposure time given the amount of light present You should select the smallest sample size that will image the entire sample This reduces the amount of unused margin around the actual slide data Sample sizes are accurate only if the camera is correctly installed in the hood If the camera is being used outside of the hood or if the slide is elevated inside the hood sample sizes will not be accurate To Capture an Image Using the Basic Capture Tab If the Basic Capture tab is not showing or if the Capture Panel itself is hidden select Basic Capture from the Acquire menu Depending on your preference settings the Capture Panel may appear on the right or left side of the Main window ues Doc IT USER MANUAL gt If another Capture Panel tab is showing you can also click the Basic Capture tab at the bottom of the Capture Panel 2 Set the exposure time sample size color and resolution to the desired settings 3 Decide if you would like to see the degree of over and undersaturation in the image If so select the Over Undersaturation check box if not clear the check box To turn off the Over Undersaturation warning on an image you ve already captured go to the
24. been padded out to make processing more efficient The 24 bit color mode has three 8 bit color channels exactly the same depth as Doc It s 8 bit color images Computer monitors are not manufactured to show greater depth ranges although they could be because the human eye really cannot perceive gradations finer than those within the 8 bit range So images with greater than 8 bit depth such as 16 bit depth have to be scaled down to 8 bit depth for display The key difference between what is shown for a true 8 bit depth image and what is shown for a 16 bit depth image lies within the choice of scaling method for the 16 bit image There are obviously no scaling choices for an 8 bit image it is already in 8 bit depth The default scaling method is to chop the low order 8 bits off of each color channel reducing the image to 8 bit across the board However a 16 bit image can also be scaled downward both by ignoring values above and below a certain range and by scaling the values inside the range to 8 bit This is a form of intensity stretch which allows the 16 bit range to be utilized more fully than with the default scaling method Depths Greater than 8 bit in Doc lt Doc It will display and manipulate 16 bit depth images correctly However the camera provided with Doc It does not capture more than 8 bit depth Most scanners also do not capture greater depth Related Topics Chapter 3 Image Window Chapter 6 Using Selection Tools Chap
25. customizable so you can include the commands you use most and remove commands you rarely use Initial Toolbar Buttons The initial buttons are r AAA E id View AD Find Llanes Hands Add Late Paleta Lare TE Clea All Lane 7r3Fle Graph Maier ar wein it Loncercration e View Lanes Bd visu Raanrs I WEA Analysts Obecks I A ho Corrector ES Lata Exp ner nalyss sckhngs En View AOI Shows or hides the Area of Interest AOI Find Lanes and Bands Searches for lanes and bands in the image Add Lane Allows you to add lanes manually by clicking where you want the new lane to be Lanes cannot be placed on top of other lanes Delete Lane Deletes the lane s you select Clear All Lanes and Bands Removes all 1D Gel Analysis Information such as lanes and bands and their IDs Leaves the annotations in place Lane Profile Graph Displays a line graph of intensity or concentration value verses position in the lane for the lane or lanes you select Molecular Weight Calibrates molecular weight with Retardation factor Rf lines and by applying standards to lanes Concentration Allows you to specify a concentration unit and mathematical relationship graph that is used to calibrate intensity to concentration View Lanes Turns on or off the lane markings View Bands Turns on or off the band markings View Analysis Objects Turns on or off all
26. esate goth nc cds E T E 46 BIST T T age hd ck EA AOA 123 R BY esc Tern ESR Gn non BE HORTaE o 1 FREGUCE Image oleada OA 57 e Mee e A te sit epic eat tile tite hat ete nu eco 58 IRelresn he VIEW ut ta iet bu sap A LL LM M Sta bu SD 115 117 119 120 PREIAUIVE FE TCQUGIIC Yc m 93 96 109 Relative Frequency LINES ii A A A A ek a 80 Remove AIL Calibration Data cesan cd 105 Remove Alesana a ds 94 REMOVE NOIS Oane a a id nia 55 Remove One R ENG aasia a a a A a A R a O 94 REMOVE SPECIES niir TELLE 54 A EUER 14 ANE KSC rr tend A 115 116 117 RES aia 57 Resize balles ns A iS a 89 PROS ZING AMO ON Sai D ORO REPRE 65 A A A a 123 A A ME TEE EO ELUCET 51 Rio esM DS Coss tects a LI UA MERE 85 99 110 113 ROLO sara eee racist tee S el UAE E ean ce MM E M MA MEE MEL 52 Rotana Text ATIOEPStIOTIS isa aia 65 S Sample Width and ARNO UNAS tados 61 abd RUS co a 38 Scale abd ARNO IO NS ota eddie 61 A cuetentaxbaieacuenceeene 38 Screen Resolution ni a A Par 1 Sedre MOS he eth Mie EM M dt cd A dd cli dla 87 88 Select Eane Prole nonne A A A AE 120 Select Lane Properties a Da idt 106 Selecung ANNOIN Sid cea Avent esants 64 Selecting Lane Informatio sessies ea aaa e a a a 106 oelecHbg Lanes erona dn pL a NUES MM MD NE DS 108 120 Selecting Other Axis Values it sait tee etai ite ru ose es oe uH UEM ere rS 109 SI DM M M D M EE 33 130 Doc IT USER MANUAL CODING ansiado laca cola ano cena 34 COPPINO lO rm 58 Selecu
27. iM DM LE 109 Y AS OPON APA Em Oe ee eR LEE 109 Z ZOOM ACCOM A aa aa aa aa aa a ait aa a ett AE 123 Shown in Image Window CaptioN iii A A A deena 18 132
28. images internally see Inside a Pixel later in this chapter Es 3 E c je e Micra Histogram for a Monochrome Image Histogram for a Color Image To Show the Intensity Histogram If the image you wish to work with is not the foremost image select it from the Windows menu or click on its title bar See Image Windows for more information From the Image menu choose Intensity Histogram The Intensity Histogram window will be displayed If the image is in color you can view the histogram for each color channel red green or blue by selecting the appropriate option below the histogram as pictured above You also can display the Intensity Histogram window using the toolbar or the shortcut menu on the Image window itself INTENSITY STRETCHING The Intensity Histogram window also contains controls for the Intensity Stretching feature Intensity stretching allows you to take an image with little differentiation in color or intensity and to stretch the intensities in the image over a greater range exaggerating their differences 40 Doc IT USER MANUAL Example of Intensity Stretch The darker image is what the camera captured The lighter image is after an intensity stretch from O to 75 Details of the dial are visible in the intensity stretched image When you stretch intensities pixel values below the lower end of the range will appear as black Pixel values above the upper end of t
29. is JPEG by default The file extension will reflect the file format e g JPG for a JPEG file Doc It supports the following formats JPEG A common lossy compression image format used to store images on disk JPEG files generally have JPG or JPEG extensions TIFF Tagged Image File Format a common image format Depending on settings TIFF can be either a lossy or a lossless compression format In Doc It it is used in the lossless mode to reduce image file size without losing integrity TIFF files generally have TIF or TIFF extensions TGA Truevision Targa image format TGA is a lossless compression format that reduces file size somewhat TGA files generally have a TGA extension BMP Microsoft Bitmap image file format BMP is a lossless format which provides some compression to reduce file size BMP files generally have a BMP extension PNG Portable Network Graphics a common image format PNG is a lossy compression format that results in very small files Files stored in PNG usually have a PNG extension GIF Graphic Interchange Format a proprietary Xerox image compression format GIF is a lossy compression format that results in very small files Files stored in GIF usually have a GIF extension JPEG PNG and GIF are lossy compression formats TIFF TGA and BMP are lossless compression formats at least as used by Doc lt TIFF can actually be either lossy or lossless Lossy compression makes small usually non visible changes
30. it monochrome This is primarily used either to remove distracting color or to prepare an image for certain types of automated analyses outside the scope of Doc It Examples of Some Manipulations Before Manipulation Flipped Horizontally Flipped Vertically 50 Doc IT USER MANUAL Cropped Embossed in Rotated pi The Image toolbar can be customized to include any or all of the manipulations REVERT This command reloads the foremost image from its last saved version If an image has never been saved it cannot be reverted All changes made since saving are discarded To Revert to the Last Saved Version 1 Ifthe image is not the foremost image select it from the Windows menu or click its title bar 2 From the File menu choose Revert A warning message box will appear pi You can customize the Files toolbar to include the Revert button 3 Click Yes The last saved version will replace the present version in the Image window DUPLICATING IMAGES This command creates an identical copy of the foremost image The new copy will appear in its own Image window If you previously have saved the image being duplicated the new copy will not inherit the con old copy s filename Instead the new copy will be an unsaved image To Duplicate an Image 1 If the image is not the foremost image select it from the Windows menu or click its title bar 51 Doc IT USER MANUAL 2 From the Image menu
31. key to select a range or by holding down the CTRL key to select multiple individual buttons Click Remove to remove the selected buttons If you remove all buttons from a toolbar it will automatically become non 9 visible 7 Once you have selected the desired buttons in the Visible Buttons list move them up or down until they are in the order you desire a To move a button or group of buttons up Select the button s and click Up b To move a button or group of buttons down Select the button s and 78 Doc IT USER MANUAL 8 Repeat steps 3 through 7 for any other toolbars desired 9 Click OK SAVING SETTINGS ON EXIT Several options are available both explicitly on the Options tab and implicitly through how you use them in the application To better adapt to your preferences you can control when implicit changes to options are made 4 Save Settings E X cave current settings Options that are changed implicitly include e View Toolbar When you show or hide all of the toolbars though the View menu Doc It stores the information and makes it your default e View Status Bar When you show or hide the Status Bar though the View menu Doc lt stores the information and makes it your default e View Capture Panel When you show or hide the Capture Panel through the View menu Doc lt stores the information and makes it your default e View Annotations When you show or hide annotatio
32. may not transfer the license rights to the software to another party TERMINATION This License is effective until terminated by either party You may terminate this License at any time by returning the Software to UVP or destroying the software and all related documentation and all copies and installations thereof whether made under the terms of this License or otherwise This License will terminate immediately without notice from UVP if you fail to comply with any provision of this License Upon termination you must destroy or return to UVP the Software and related documentation VIII Doc IT USER MANUAL LIMITED WARRANTY AND DISCLAIMER UVP WARRANTS THE CD ROM ON WHICH THE SOFTWARE IS RECORDED AND THE SOFTWARE AND RELATED DOCUMENTATION TO BE FREE FROM DEFECTS IN MATERIALS AND WORKMANSHIP UNDER NORMAL USE FOR A PERIOD OF NINETY 90 DAYS FROM THE DATE OF PURCHASE AS EVIDENCED BY A COPY OF THE SALES RECEIPT OR PACKING SLIP UVP S ENTIRE LIABILITY AND YOUR EXCLUSIVE REMEDY WILL BE REPLACEMENT OF THE DEFECTIVE CD ROM S SOFTWARE AND RELATED DOCUMENTATION OR REFUND OF THE PURCHASE PRICE AT UVP S ELECTION UPON RETURN OF THE CD ROM SOFTWARE AND RELATED DOCUMENTATION TO UVP WITH A COPY OF YOUR PROOF OF PURCHASE UVP WILL HAVE NO RESPONSIBILITY TO REPLACE A CD ROM DAMAGED BY ACCIDENT ABUSE OR MISAPPLICATION THIS WARRANTY GIVES YOU SPECIFIC LEGAL RIGHTS AND YOU MAY ALSO HAVE OTHER RIGHTS WHICH VARY FROM JURISDICTION TO JURISDICTION YOU E
33. on the image where you would like to place the upper left corner of the annotation A view of the new annotation will follow the mouse as you move showing you what it would look like If you change your mind about adding the annotation at this point simply press the ESC key 4 Click the position on the image where you would like the lower right corner of the annotation to be The annotation will be drawn To Create an Angle Measure Annotation 1 From the Tools menu choose Angle Measure 2 If desired select the color font size and formatting bold italic underline from the Formatting menu 3 Click the first point A line will follow your mouse until you click a second point If you change your mind about adding the annotation at this point simply select a different tool from the Tools menu 4 Click the second point Again you may cancel the new annotation by pressing the ESC key A second line and the number of degrees will follow the mouse as you move it until you select the third point 5 Click the third point The annotation will be drawn 63 Doc IT USER MANUAL p The Tools toolbar can be customized to include the annotation tools that you frequently use THE TEXT EDIT WINDOW Text annotations allow you to place labels on an image to describe or to name a feature of the image Use the Text Edit window to enter the text The Text Edit window appears whenever you add a new Text annotation It also app
34. other images in Doc It Copy does not affect the image in any way To Copy an Entire Image 1 If there is a selection on the image click away from the selection once to cancel it 2 Choose Copy from the Edit menu To Copy a Selected Region Within an Image 1 Select the desired region using one of the selection tools 2 Choose Copy from the Edit menu 34 Doc IT USER MANUAL Whether you copy an entire image or a selected region of an image Copy also is available by using the Ctrl C accelerator key by using the Copy button on the Toolbar and by using the shortcut menu on the Image window itself PASTE This command takes an image from the clipboard and imports it into Doc It displaying it in a new Image window mo Paste can also be used on text in which case it acts in the standard Windows fashion To Paste an Image rm Paste is only available if there is an image on the clipboard ps PASTE SPECIAL This command allows an image on the clipboard to be merged into the current image It is useful for adding comparison or reference information into an image for making composite images and for testing two images against one another for motion The following merge modes are available in Doc lt ET Blend mixes the incoming image with the current image in a selected proportion If the proportion is set to 100 pixels in the incoming image replace those in the existing image without mixing
35. see gross large scale detail more easily after the edges have been blurred because details that may have been obscuring it are removed To Blur an Image 1 Ifthe image is not the foremost image select it from the Windows menu or click its title bar 2 From the Image menu choose Manipulation and then Blur Blurring a large 55 Doc IT USER MANUAL image may take a few seconds cun If the image has not yet been saved you will be prompted one time to save it E before the first manipulation you select EMBOSS This manipulation gives an image a chiseled in stone look Edges take on a three dimensional 3D appearance making them stand out vividly Example Before and After Embossing Emboss can be performed from any of eight cardinal directions Conventionally these are referred to as North up Northeast East right Southeast South down Southwest West left and Northwest The easiest way to think of the direction of the embossment is as the location of a strong light source around the image For example if you select North the image will appear as if it is illuminated with a strong light from the top Therefore horizontal edges will be strongly lighted on the top edge and shadowed on the bottom and vertical edges will tend to disappear Diagonal edges will be shadowed in direct proportion to how closely they are horizontal Alternatively if you select East vertical lines will be shadowed on the le
36. several screen pixels are used to show one actual pixel This generally makes detail easier to see Zoom factors less than 100 mean that the image has been scaled down This makes it possible to see more of the image in the Image window 123 Doc IT USER MANUAL INDEX 1 THE PATA SUS TV VV isos oia 80 Po A ee eee ee eee 80 ES AVS cos cp es ce ee eet ea ee ea ecclesia ce ce eae oe ee ee t 89 Concentration Calcula io 99 pall a8 lle py Lane Ad 86 Lane Proe Gra pl met cpm 108 MENUS raien na e N E 80 REDONS ete a aCe eo ee a een 106 A eacaeae bes 82 Ss E 85 A PACE CIS T ALON ING S as catalan 12 A A pL iM 12 Ada Bandas Maida os 89 AOG EINO aera ete EUM a TES UE Pee SOE M Le pM 82 AC SPEI S o tutu LM UU I A E iu M I uM E LM hu 93 PP A Lui pM LM LM E pi 102 BARI ERU 102 Advanced Capture Tabsssste iuri otto a cebat io cte i e Dieci 23 as Dart or Ex DION i osi nicis da o be esi endet fea 18 Advanced Capture Templates usina utet cue to ute ie D tube dll nuda ee 26 After Capture gode TRE RET 76 A 76 PAA ON 1 POP E O R 92 ANO ANAWYSIS LODO se 82 O O O mutual ances weneeoaate 111 A TD UTE 120 Analysis A mI 113 Analysis Bands Fixed Report usina iia did 119 Analysis Lanes Fixed ROD unid AS baad E 118 ANalYsIS SCUINGS ista a tedio 107 114 Anchor ENGS us ccbe tae o eae oe 104 AMO INSTR Sut A is 60 82 Aci AAA o ROMO Em E O 62 VS STNG IP O 66 O A da
37. using a 46 Doc IT USER MANUAL natural light spectrum e Blue Colors all intensities from black to bright blue e Cyan Colors all intensities from black to bright cyan e Green Colors all intensities from black to bright green e Magenta Colors all intensities from black to bright magenta e Red Colors all intensities from black to bright red e Yellow Colors all intensities from black to bright yellow To Apply a Pseudocolor 1 Ifthe image is not the foremost image select it from the Windows menu or click on its title bar 2 Ifthe Capture Panel is not showing or is showing a tab other than the Effects tab choose Effects from the Image menu pi You can also show the Effects tab from the toolbar 3 From the Pseudocolor drop down list select the desired pseudocolor The image will be colorized as desired To Remove a Pseudocolor 1 Ifthe image is not the foremost image select it from the Windows menu or click on its title bar 2 Ifthe Capture Panel is not showing or is showing a tab other than the Effects tab choose Effects from the Image menu pi You can also show the Effects tab from the toolbar 3 From the Pseudocolor drop down list select None The image will no longer be colorized ZOOMING AND PANNING By Zooming you can magnify part of the image making small details more visible Once you have zoomed in on the image the entire image will no longer be visible in the window You can chan
38. where you would like the new band to be If the color of the horizontal line is green you can place the new band where the cursor is If however the color is red there is already a band at this position and you cannot place another band there Move the mouse until the line appears green 3 Click the left mouse button to place the new band Note that you can place as many bands as you like as long as this feature is on 4 When you are finished placing your band s click on Edit 1D Objects under the 1D Analysis menu Moving and Resizing Bands Just as with lanes Doc lt allows you to move and resize bands according to where you want them To Move Bands To Move Bands on the Image Window 1 Under the 1D Analysis menu select Edit 1D Objects 2 Select the band you wish to move by clicking on it Controls handles will appear around the band 3 Drag the box up or down within the lane until it appears where you want it Note that you can only move a band between the bands above and below it not beyond other bands To Move Bands Using the Lane Profile Graph 1 Under the 1D Analysis menu select Lane Profile Graph The graph appears in a new window 2 Ensure that Band Peaks and Band Extents are both selected Under the graph find the band markers Drag the peak marker of the band the large marker in the middle of two smaller markers to the place you desire that band Note that the markers on the graph change position
39. which is a portion of the price you paid the software including any images incorporated in or generated by the software and data accompanying this License the Software and related documentation are licensed not sold to you by UVP Inc UVP UVP does not transfer title to the Software to you this License shall not be considered a sale of the Software You own the CD ROM on which the Software is recorded but UVP retains full and complete title to the Software on the CD ROM and the accompanying documentation and all intellectual and industrial property rights therein This non exclusive and personal License gives you the right to use and display this copy of the Software You must treat the Software like any other copyrighted material You may not copy the Software or the written material accompanying the Software RESTRICTIONS The Software contains copyrighted materials trade secrets and other proprietary material You may not re sell decompile reverse engineer disassemble or otherwise reduce the Software to a human perceivable form Except as provided for in this License you may not copy modify network rent lease or otherwise distribute the Software nor can you make the Software available by bulletin boards on line services remote dial in or network or telecommunications links of any kind nor can you create derivative works or any other works that are based upon or derived from the Software in whole or in part You
40. you can preview the result 4 Select the desired merge operation Blend Add or Subtract 5 Ifusing Blend set the desired blend percentage 6 Click OK 36 Doc IT USER MANUAL 7 Moving the mouse over the existing image position the merge as desired The merge results or positioning frame for Preview Frame Only will be previewed as you move the mouse You will be positioning the upper left corner of the incoming image 8 When you reach the desired position click the mouse button once Merges that involve large images may take a few seconds to complete Related Topics Chapter 3 Image Windows Chapter 8 Effects Tab Chapter 9 Manipulations Chapter 9 Crop IATa Doc IT USER MANUAL CHAPTER SEVEN SPECIAL FEATURES Rulers Magnify Tool Intensity Histogram Intensity Stretching Understanding Pixels Related Topics There are a few special features available in Doc It which are not part of any of the other groups described in Help These are e Image Rulers which are calibrated automatically for images captured through the camera and Darkroom Hood e The Magnify Tool which allows parts of an image to be magnified at the click of a button e The Intensity Histogram which graphically displays the distribution of intensities in an image and allows intensities to be stretched RULERS Tt riasectacrreii Gases LARA n In Doc It you will find rulers at the top and left of each Image O AREA win
41. 0 VIEWING And Filaing APInotallolis s t eoa tt n et ia det 61 To Show or Hide Annotations for an Image occccccocccnconccncononcnnconanoncnnanononnonnnnnnaronconanennnnanens 61 Types O ieu P LEE 61 Creating AAINMOLATIONS aces da aida 62 To Greate a TexPAnnotallQliz cu A A oda 62 To Create a Line or Length Measure Annotation cccccocncncccoconoconcnnconononnononnnnonnarononnncnnonanens 63 To Create a Rectangle Ellipse Highlighter or Area Measure Annotation 63 To Create an Angle Measure AnnotatiON cccooncnccccnnnnccnoccncononcnnononnoncnnonononnoncnnnnaronnonanennnnanens 63 The Text EdiE VWIIgOW as sds inaccurately tess A ut o c iude 64 To Edit the Text of a Text AnnotatiON ooccccoccccocncoconococonocononononnnnonannnonnnnonannnonnnnononnnenanens 64 Selecting ANMOLANOMS er MR P M ciiiids 64 To Sslect anExisundAnOotellgby teni ca ben etus toe tene a bc e oet 65 Moving And Resizing Annotations ccoccccccccncconcconccnnconnconnnnnnnnnnnnnonanonannnnncnnonnninnninons 65 TO MOVe an XISTING ANNO OM c 65 To Change the Points of an Existing Line Length Measure or Angle Measure Annotation 65 To Resize an Existing Rectangle Ellipse Highlighter or Area Measure Annotation 65 To fxotate a Text ArnolallOD so iuo ted su tien e ccoo 65 qeluanudsrop risieyziiol ee cL 66 To Change the Format of an Annotati0N ooccccconnncccoc
42. 1 Ifthe image is not the foremost image select it from the Windows menu or click its title bar 2 From the Image menu choose Manipulation and then Flip Vertically crm If the image has not yet been saved you will be prompted one time to save it E before the first manipulation you select DESPECKLE This manipulation removes single pixel flaws called artifacts from an image For many reasons the image capturing process and hardware might misread isolated individual pixels as either white or black The Despeckle manipulation mathematically identifies and removes these loner pixels There are two issues to be aware of with Despeckle First if your image has actual desired single pixel bright or dark areas the operation will not be able tell these from artifacts and it will remove them Second the mathematics of the operation can cause some edge pixels to be identified as speckles resulting in slight blurring on some images To Despeckle an Image 1 Ifthe image is not the foremost image select it from the Windows menu or click its title bar 2 From the Image menu choose Manipulation and then Despeckle Despeckling a large image may take a few seconds 54 Doc IT USER MANUAL crm If the image has not yet been saved you will be prompted one time to save it E before the first manipulation you select REMOVE NOISE This manipulation removes periodic patterned noise from an image Patterned noise is r
43. 3 Cane Prole rapi deter da die 80 82 83 99 106 107 108 Laned roDEnleS sth ui eR Le uui I i uu E S M EM E M 106 Lane Width Constant Across All Lanes coooncccccnnccccnnococonocononononnnnnnnnonannonannnonannnnnnnnnnnnnnnnanons 117 LANES T EE OE Dm 114 Last Saved VerslO a a A mtem s a T Rp eee 51 Layout DUtO Ma e 113 EcastSquares MI Et 104 Least Squares Quadralic 2 eee eai eo AS 104 128 Doc IT USER MANUAL lossless COMPrESSIO usas isla tacita 122 LOSSY COLDDIeSSIOL iuo essi bl vna dis 122 M Macro MOJE ton e e ELE ese ed 123 Magniy NONE LT c RH MER 16 Maln WINGOW NER ERROR RTT Er Sl O Oa os O aca ata altace 11 MER m TT 49 VIG A r R lvo d sao Le afiteu Co Eo a a Cue MS a M dio o ds tuba OL cuoco 02 A Ec 99 A A Mm UE 58 TNS SOC d me HM T CLE o4 DUDIC dign ce cn E UO DUE SU E 51 EMDOS A eee ee ee eae 56 PIRON ZONAI RE o4 Pip VY ELC UY cc PES o4 Recovering from with Revert lssssesssssssssseseeee nennen nenne nennen nnne nnns na ananas rra n a snas nna 51 Reduce to MonDOoODFOFigin i ada A A nd cM al uda 58 nn eens eee Seat dees eee aa eee of e HY 52 nn i anes EN 55 Manualintensiy Siete hierna s 40 Mantal Search ia 88 Massi A os 85 106 118 Memory Re qui Me Saa a AA AS AAA 1 NUCTODIO LO Vasari AAA 123 NICTOSCO Vii A AAA AAA 123 MICLOS OM EXCA e EET T LL TEE 116 VifelIsieib rz
44. 4 Click OK To see what the system would look like with changes click Apply instead CUSTOMIZING TOOLBARS You can select which buttons will appear on any of the toolbars offered in Doc It This allows you to place frequently used buttons on the toolbar where they are available with just one click is Doc IT USER MANUAL A Preference Dptene Toolbar Toobar Fis F Tools sible Arado Auttone Vibia Buliort Japas a gt Oper Ey Clubs IL save A arem As Print Frm rar nn To reset the toolbars to the program s original defaults click Factory Settings To Customize Toolbars 1 From the Files menu choose Preferences You can also double click the toolbar or select Customize Toolbars from the Toolbar Shortcut menu 2 Ifthe Toolbars tab is not showing click Toolbars at the top of the window 3 Select the toolbar you wish to customize 4 f you want to hide the entire toolbar clear the Toolbar Visible check box If the toolbar is hidden and you now want to see it select this check box 5 From the list of available buttons select one or more buttons to add You can select multiple buttons either by holding down the SHIFT key to select a range or by holding down the CTRL key to select multiple individual buttons Click Add to add the selected buttons to the toolbar 6 From the list of visible buttons select one or more buttons to remove You can select multiple buttons either by holding down the SHIFT
45. Concentration Calibration Selecting Data Points Selecting Curve Type Removing Concentration Calibration Related topics OVERVIEW Having sized and moved lanes and bands you are now able to ask Doc lt for concentration calculations In this chapter you will learn how to do the following e Correct background for overexposure or uneven exposure of light or chemicals e View a background corrected image e Show the concentration graph for calibration e Select data points to plot on the graph e Select the type of curve to fit to the data points and e Remove all concentration calibration data BACKGROUND CORRECTION Background Correction Options To account for possible variable illumination or overexposure during image capturing Doc lt offers options to apply mathematical background correction All these options generally remove background noise and elevated levels of pixel intensity due to excess exposure highlighting data General Procedure for Background Correction Selection 1 From the 1D Analysis Menu select Background Correction A new list appears 2 From the list select which type of background correction if any Doc It should perform 99 Doc IT USER MANUAL Viewing Background Correction in the Lane Profile Graph 1 From the 1D Analysis Menu select Lane Profile Graph 2 On the graph select the XXX Background Correction checkbox XXX is the name of the correction that is being applied
46. Doc It ACQUISITION AND 1D ANALYSIS SOFTWARE Installation and User Instructions NOTE This manual includes Doc lIt acquisition and 1D analysis functions If you did not purchase the Doc It 1D Analysis Software module the analysis menu functions will be grayed out and not usable The analysis functions can be enabled with the purchase of a Doc It 1D Analysis Software upgrade 81 0217 01 Rev B Doc IT USER MANUAL TABLE OF CONTENTS CHAPTER ONE WELCOME To Doc It o 1 Overview Of Application Features occcocccocccocccoccconnooncoonooonconnnncnonnnnnnnonnnonnnonnnnnnnnnnnons 1 System FREGUISC mens a 1 Installation InStructlOnS nisse ta Ca D ER NE elt eio seateiaentenvals 2 Installi g the DoOc IESOTIWATEe uds toute idee fe dou eo didas 2 To Set Up the Camera Hardware for the First Time c ooccccccccncccnnococnncnonnnononnnonnnncnonncnonononos 2 To Connect the Camera to the Computer cccooccccoccncccccncoccncconcnccononononononannnonannnonnnononnnononnnonanons 3 To Install the Camera Driver Software cccooccccooccccoccccocnconcncoonnconnnonononnnnnonnnononnonrnnoncnnncnconnnnnnos 3 To Insert the Camera into the Darkroom Hood ooccccoccnccccnnccoconocononononononnncnnnnnoconononanonenanonos 3 TosAttach the Securty KGy ee eee oro Ut el p as E eon ara i aede eed tes 3 HOW To Start The Appian isc iiie aad eain dace vna d Cade Cae Re a ved edd 4 Ney Managermelnzs iioii istctasie disi o iO ad 4 TO leem
47. E AUE 31 The dImage File aui ct Ve daa a su aee Dl aut 31 The Extended Attributes File occcooocccoccncoccncccconcccnonocnononcnnnconanononanononannnnnnncnnancnnannnss 31 CHAPTER SIX EDITING 5o eu auu eu S Eun av a caian 32 SII LT 32 UNO ROO M das 32 To Undo the Last Change to an Image sees nennen 32 To Redo the Last Change to an Image coooccncccnccnnccnconccnnnoncnnoncnnnnnanononnnnnnnnnncnnnonarnnnonancnnnnanens 33 USING Selection Tod Sua ads 33 TOS CI cha REJO RE TL dea 33 FOAGIUSE The Selec PT TRES 33 To CanGeli Ihe Selecionar od 34 COD este ster ee nee er ME A eR eS eRe 34 To Gopy an Entire Mage a AAA A AAA A Gitta 34 To Copy a Selected Region Within an Image cccoocccncccccncccnccnncnnncnncnnononnnnonnnnonnnnnnonanennnnanons 34 A TU UU m 30 ROP ASte AN lIMaG cT DER 35 Paste opel M CRT OT IU 35 TOMergesiWO IMages isis TEE 36 Doc IT USER MANUAL CHAPTER SEVEN SPECIAL FEATURES ua as 38 A O oo o A 38 Lo Show or Hide the RUIGIS ui id 39 Magniy TOO etr cluan eos 39 To Use the Magnify TOOL uisi n e Lat o alee NDS sia 39 intensity Histogram escrita ti dsd 39 To Show the Intensity Histogram sion anios 40 Mensy Sreten m 40 To Stretch IMCCNSIWSS oo e eto t LO eene defin flies esee eaves 41 To Turn Off Intensity Stretching acd cunc asit dur sa tatio aee gu qo Gu Unina eua c
48. E HELP The Online Help system provides explanations of what each system feature is why you might use it and how to find and use it It also defines terms used in Doc It and goes into depth on certain features to explain how they work Showing Help You can use Help in the following ways e By pressing the F1 key This will show you information about the current Doc It window you are viewing e From the Help menu by choosing Doc It Help This will show the Table of Contents pi Selecting a toolbar command acts just like its menu counterpart Clicking the Help button on the toolbar is the same as choosing Doc It Help from the Help menu Using Help No matter how you access Help you can e View the Table of Contents by clicking the Contents tab and then view any topic by double clicking on it e Search for a topic in the Index by clicking the Index tab and typing a search word e Search for any word or phrase by clicking the Search tab typing the search word or phrase and then clicking the List Topics button e Add a current topic to a list of Favorites so that you can easily find it again by clicking on the Favorites tab and then clicking the Add button at the bottom You can also view any existing Favorite by double clicking it in the Favorites list In many areas of Help you can navigate through several related topics by clicking the Next and Previous buttons or the name of the topic in the Browse Sequence area at the top righ
49. Edit wndow will appear 4 Type the desired text in the text box 5 Click OK The Text annotation will be displayed at the position you indicated To Create a Line or Length Measure Annotation 1 From the Tools menu choose either Line or Length Measure as appropriate 2 If desired select the color line style and line thickness from the Formatting menu For a Line annotation you can also select whether to use arrowheads For a Length Measure annotation you can also select formatting bold italic underline 3 Click the position on the image where you would like the annotation to begin A line will follow the mouse as you move it showing you what the new annotation would look like If you change your mind about adding the annotation at this point simply press the ESC key 4 Click the position on the image where you would like the annotation to end The new annotation will be drawn To Create a Rectangle Ellipse Highlighter or Area Measure Annotation 1 From the Tools menu choose the appropriate tool Rectangle Ellipse Highlighter or Area Measure The Select Rectangle and Select Ellipse tools are not annotation tools They 5 appear further down the menu 2 If desired select the color line style and line thickness from the Formatting menu With Highlighter annotations you can only select color For an Area Measure annotation you can also select formatting bold italic underline 3 Click the position
50. Histogram and the Effects tab of the Capture Panel and commands to manipulate and to duplicate the image e Tools Contains a list of the tools you can use to interact with an image including Selection tools the Magnify and Image Scale tools and Annotation tools e Formatting Contains selections to control the appearance of an annotation including color and line style e 1D Gel Analysis Contains commands to work with lanes and bands to view reports of lanes and bands and to perform calculations e Windows Contains commands to organize Image windows e Help Contains Key Management as well as access to this Help system Rearranging Toolbars You can expand or contract a toolbar or place it on a new row in the toolbar space by dragging the raised area at the beginning of each toolbar 247 Doc IT USER MANUAL CAPTURE PANEL The Capture Panel consists of three tabs The commands on these tabs Pimp ta aj na Sie are not available anywhere else Lai hamer E Sew ten a e The Basic Capture tab gives you simple and quick access to the eee most commonly used camera features p Coba Tapia citado e The Advanced Capture tab gives you both complete control of all Morne at camera features and access to the Capture Template system so that groups of settings can be reused as templates e The Effects tab offers the most commonly used image tools including brightness contrast Zoom and pan Litas epe Sa
51. The graph will now display the background correction in the selected lane as a dotted line 3 On the graph select Corrected Values The graph will now display the remaining intensities after background correction has been applied 4 You can also change the background correction method on the Lane Profile Graph Select the desired method from the drop down on the right side of the graph Viewing the background correction for several lanes and methods is often a good way of selecting an appropriate correction method Specific Correction Options Doc It offers five background correction options No Correction Selecting this option on the menu leaves the image uncorrected for overexposure as is Straight Line Selecting this option tells Doc It to place a straight but not necessarily horizontal line under the lowest points at the beginning and end of each lane Doc It then removes the area of the graph under the straight line so that all remaining values are emphasized Straight line correction tends to correct well for overexposure and for variable illumination that is focused on an edge or corner of an image Joined Valleys Selecting this option accentuates the data by telling Doc It to join lines between the lowest point or valley before the first band between each pair of bands and after the last band Intensities above the valleys band data are emphasized Joined valleys can perform well in a variable illumination cond
52. Then click on Copy 4 The Edit window will appear Click on Add or Edit to edit what you wish in the copy Then click on OK In the first wndow another standard appears entitled Copy of whatever standard you chose to copy APPLYING A STANDARD TO A LANE Lahbrate Standard to Lane F Calizaie Moleculer Weight Standard Calibrating a Lane ac Select the lane you wish to calibrate From the 1D Analysis Menu select Lanes and then select Calibrate Molecular Weight A new window appears From the list of standards choose the standard you wish to use Ifthe standard is not on the list add the standard to the list see Managing Weight Standards Press Next which is the gt button A new screen appears In the new screen you can adjust the weights to match the bands that actually appear Complete instructions for this appear below Click OK to save the calibration pi You also can access this feature using the 1D toolbar 96 Doc IT USER MANUAL Using the Stretch Factor The stretch factor establishes a mathematical relationship between the weights to describe their relative movement The larger the stretch factor the more lighter weights move in relationship to heavy ones The smaller the stretch factor the less the lighter weights move A stretch factor of 1 0 indicates linear movement weights move in direct proportion to their relative weights To adjust the weights to ma
53. Tools menu The Edit menu also offers a Cut feature that can be used while editing text in Doc It Cut does not work on images UNDO AND REDO The Undo command will undo the last material change made to an image Material changes include all manipulations and use of the Paste Special command Changes made through the Effects tab e g Zooming panning or changing brightness or contrast cannot be undone with the Undo command Changes to annotations also cannot be undone The Redo command reverses the last Undo To see what the last material change did in detail you can alternate between Undo and Redo Changes made on the Effects tab do not permanently change the image To reverse these changes click Reset on the Effects tab To Undo the Last Change to an Image 1 Ifthe image is not the foremost image select it by clicking the window title bar or by selecting its title from the Windows menu 2 From the Edit menu click Undo The former version of the image will be restored 239 Doc IT USER MANUAL pi If you have made several changes to an image that was saved you can return to the saved copy using the Revert command If you decide that you want the last change after all you can reinstate it with the Redo command To Redo the Last Change to an Image 1 If the image is not the foremost image select it by clicking the window title bar or by selecting its title from the Windows menu 2 From the Edit menu
54. What the background color is e Whether there is background correction e The disc radius of the disc if you used Rolling Disc e Whether the anes are constant e Whether there is a lane summary e Whether the lanes are straight e The unit name of the concentration e The concentration curve type e The intensities of the calibrated concentration e The ranges of the calibrated concentration In the Lanes tab you can find the following e Lane D e Lane Name e Where the lanes start and end e Lane width e Lane mass e The maximum intensity in the lane e The volume of the intensity in the lane 113 Doc IT USER MANUAL The concentration maximum and volume and The number of bands In the Bands tab you can find the following The band D The name of the band The molecular weight of the band The Retardation factor The top peak and bottom values of the band The intensity maximum volume percentage and mass and The concentration maximum volume percentage and mass The Data Explorer also has four buttons that give you further options zb The Layout button brings up the Tabular Layout window The Filter Data button allows you to select which data to include in the tabular report for this report The Print button first brings up the data selection window for the report after you select which data you want in the report click OK and the report itself will open up with options for printing The Exp
55. XCLUSION MAY NOT APPLY TO YOU LIMITATION OF LIABILITY UNDER NO CIRCUMSTANCES INCLUDING NEGLIGENCE SHALL UVP BE LIABLE FOR ANY SPECIAL OR CONSEQUENTIAL DAMAGES THAT RESULT FROM THE USE OF OR THE INABILITY TO USE THE SOFTWARE OR RELATED DOCUMENTATION EVEN IF UVP OR A UVP AUTHORIZED REPRESENTATIVE HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES SOME JURISDICTIONS DO NOT ALLOW THE LIMITATION OR EXCLUSION OF LIABILITY OR CONSEQUENTIAL DAMAGES SO THE ABOVE LIMITATIONS OR EXCLUSION MAY NOT APPLY TO YOU IN NO EVENT SHALL UVP S TOTAL LIABILITY TO YOU FOR ALL DAMAGES LOSSES AND CAUSES OF ACTION WHETHER IN CONTRACT TORT INCLUDING NEGLIGENCE OR OTHERWISE EXCEED THE AMOUNT PAID BY YOU FOR THE SOFTWARE GOVERNING LAW AND SEVERABILITY This License shall be governed by and construed in accordance with the laws of the State of California without giving effect to any principles of conflicts of law Any actions suits or proceedings instituted in connection with this License the CD ROM the software and or related documentation shall be instituted and maintained exclusively in the Superior Court for the State of California County of Los Angeles or in the United States District Court for the Central District of California By entering this License you hereby consent to the venue and jurisdiction of the aforesaid courts If any provision of this license shall be unlawful void or for any reason unenforceable then that provision shall be deemed
56. XPRESSLY ACKNOWLEDGE AND AGREE THAT USE OF THE SOFTWARE IS AT YOUR SOLE RISK AFTER THE NINETY 90 DAYS THE CD ROM SOFTWARE AND RELATED DOCUMENTATION ARE PROVIDED WITHOUT WARRANTIES AND OR CONDITIONS OF ANY KIND EITHER EXPRESS OR IMPLIED EXCEPT AS PROVIDED ABOVE UVP EXPRESSLY DISCLAIMS ALL OTHER WARRANTIES AND OR CONDITIONS EXPRESS OR IMPLIED WITH RESPECT TO THE CD ROM SOFTWARE AND RELATED DOCUMENTATION INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIEES AND OR CONDITIONS OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE UVP DOES NOT WARRANT THAT THE FUNCTIONS CONTAINED IN THE SOFTWARE WILL BE UNINTERRUPTED OR ERROR FREE OR THAT DEFECTS IN THE SOFTWARE WILL BE CORRECTED AFTER THE NINETY 90 DAYS FURTHERMORE AFTER THE NINETY 90 DAYS UVP DOES NOT WARRANT OR MAKE ANY REPRESENTATION REGARDING THE USE OR THE RESULTS OF THE USE OF THE SOFTWARE AND RELATED DOCUMENTATION IN TERMS OF THEIR CORRECTNESS ACCURACY RELIABILITY OR OTHERWISE THE LIMITATIONS OF LIABILITIES DESCRIBED IN THIS SECTION ALSO APPLY TO THE THIRD PARTY SUPPLIERS OF MATERIALS USED IN THE SOFTWARE NO ORAL OR WRITTEN INFORMATION OR ADVICE BY UVP OR UVP AUTHORIZED REPRESENTATIVE SHALL CREATE WARRANTIES AND OR CONDITIONS OR IN ANY WAY INCREASE THE SCOPE OF THIS LIMITED WARRANTY YOU AND NOT UVP ASSUME THE ENTIRE COST OF ALL NECESSAY SERVICING REPAIR OR CORRECTION AFTER THE NINETY 90 DAYS SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OF IMPLIED WARRANTIES SO THE ABOVE E
57. a 66 MOVING el NOI SIZING Pe EO E E E taunts 65 EEE E eae cocta iam IM MI M tL EM I AE 64 TYPES Of T 61 Viewing and HI IG 61 Area Between AMOS a e od eae 85 99 Area Between LINES ste tena uda mac tL dus Ia M ELI UM ES eae ol 82 o eee ee 122 Removing WIT Despeckle voii a aaa o4 Autoinauc Intensity St e si da tia IuUPIO 40 AULOMmaticARt Line Determination sig sca c coc 92 PASCO ica 110 124 Doc IT USER MANUAL B Backdroundd4 olor enema ear ota EI eee ee 110 Background COMECHOM xc istuc i ea cee poro Pere Medie uot eM M Map Un EAE QUI ERES 82 85 101 113 Background Correction Mena ido 99 Background COLITGecloris iii is A E 82 99 110 120 zig mec M 111 o SA uuu IM ML E E 110 120 srienpeseumu ere 85 107 saec 104 Sana co TERT 119 PAG dcc T RTT TTE TTE ER 110 120 Band diee ci cic a TE E T DO TD UTER 107 A 113 114 Bands OMY S 87 88 Basic Capre Tabs cU 22 as DAMON EX DION CR ce da 18 sl v4l RETE EE 104 zit PIE E 31 122 Blacicana iler toe es anit 2 123 A te seshoal 99 Si ge NEN LP 31 122 A CERAM 104 C Calculated Valles estatal aa 102 Callbrate GoOncenta londres 82 101 INS teo at m 101 Calibrate Intensity WINCOW sias sapevo dea ioo dalla 102 104 Calibra
58. age layout Your printer may offer additional configuration options 4 Click OK Related Topics Chapter 11 Image Information ls Doc IT USER MANUAL CHAPTER THIRTEEN CUSTOMIZING Doc IT Overview Multiple Profiles Options Customizing Toolbars Saving Settings on Exit Related topics OVERVIEW Doc lt is designed to fit your workplace work style and work habits primarily by allowing you to customize your settings There are three types of customized settings e Implicit Settings Doc lt stores information such as the last text you entered for a text annotation and uses it as a default for the next one You do not need to do anything to benefit from these settings e Options Certain aspects of the system such as whether toolbars are shown and whether the Capture Panel is shown and where right or left side are options that you can set through the Preferences window You also set options implicitly as you use the system and then save them when you exit e Toolbars Through the Preferences window you also can configure which commands appear on the toolbar which can speed up your work considerably MULTIPLE PROFILES Profile support allows you to create and maintain your own screen settings and preferences in Doc lt By default Doc It enables the Multiple Profile Selection This means you will be asked to select a profile to load at the start Whatever profile you select will reload the configuration fo
59. ally and immediately fits the curve model you choose to the data points as you select the models Directly underneath the Curve Model e M dudo Fi E3786 list Doc It shows the Goodness of Fit for the Concentration fo ss Point ER curves as they are graphed The goodness of fit is Curve Model I Anchor Lines found from the coefficient of determination also ESpline T Paint Mame known as r squared The goodness of fit value ranges between 0 0 and 1 0 A value of 1 0 for the j goodness of fit indicates a perfect fit UT 22 00 e Doc lt also allows you to choose to see the line or 86 10 d curve graphed either on its own or with additional information In the Display section underneath the Goodness of Fit indicator you can choose to display Point Values Anchor Lines from the data points down to the x axis and the Point Name assigned from the band IDs Note that you can Enter data points by selecting bands from the image select to see one or all of these three Display options Cancel E p fa E n e E ll C O o Intensity 2235 104 Doc IT USER MANUAL REMOVING CONCENTRATION CALIBRATION To remove all calibration information including data points plotted on the graph and curve lines simply go to the 1D Analysis menu select Concentration and then select Remove All Calibration Data A window will pop up asking you to confirm that you wish to remove all calibration data Click on Yes or No By clicking on Yes al
60. and add lanes by moving resizing and curving or straightening them e How to modify and add bands and e How to clear the image of all lane and band information NAVIGATION 1D Gel Menus Doc It offers the following 1D Analysis Menu on the main toolbar 1D Analysis Window Help The 1D Analysis Menu Contains the following features Lane Profile Graph e Lane Profile Graph Creates a line graph of one or Edit 1D Objects more of the lanes that you select in different colors Find Lanes and Bands In the graph you can also display band peaks band eem extents and corrected values Bands Edit 1D Objects Selecting this command allows you Relative mobility RF Lines to change lane width and height and band height Background Correction Find Lanes and Bands Finds lanes and bands or Concentration bands only after lanes are in place either manually or automatically Clear All Lane Band Information Lanes Allows you to change the lanes in multiple Data Explorer ways 10 Analysis Settings Bands Allows you to change bands in multiple ways 80 Doc IT USER MANUAL Retardation factor Rf Lines Allows you to create and change Retardation factor Lines in multiple ways Background Correction Allows you to choose whether to correct the background on the image through several methods You can also choose to display the Corrected Image Concentration Allows you to calibrate the intensity levels on the image to a con
61. and to keep a control version to compare the effects of various manipulations cro A record of manipulations performed on an image is kept in the image s Image History O Doc It supplies the following manipulations e Rotate Rotates the image around its center useful for aligning images taken with a 49 Doc IT USER MANUAL crooked gel e Flip Horizontally Mirrors the image right for left correcting for an upside down gel e Flip Vertically Mirrors the image top for bottom also correcting for upside down gels in the other direction e Despeckle Removes single pixel flaws in the image called artifacts e Remove Noise Removes periodic patterned noise in the image e Sharpen Enhances edges in the image making them more pronounced This can make small features easier for you to see e Blur Dulls edges in the image making them less visible This can make large features easier for you to see e Emboss Gives the image a chiseled in stone look The resulting 3D appearance makes certain edges and features more obvious to you e Resize Enlarges or reduces the image in size You can use this to reduce an image s size so that you can work with it more easily Reducing an image also takes less memory and disk space e Crop Removes parts of the image from the edge This can be used to remove areas outside of a rectangular gel captured during the imaging process e Reduce To Mono Removes color from the image making
62. anes and bands Ensure that the checked color is the correct color for the image e Background Correction In this feature select whether to have any background correction at all or to correct the background through one of the following Straight Line Joined Valleys Area Between Lanes or Rolling Disc If you select Rolling Disc you may change the size of the disc radius between 0 and 50 gt You also can access this feature using the 1D toolbar FINDING 1D GEL LANES AND BANDS In a 1D gel image various chemicals are placed in wells at the top of the gel Different methods are then used to distribute these chemicals across the gel in lanes Concentrations of chemically similar components form bands within each lane In this section you will find step by step processes for finding lanes and bands within your image You also will learn how to identify your area of interest and how to perform both automatic and manual searches for lanes and bands as you progress in your analyses Identifying Area of Interest By selecting an Area of Interest you are telling Doc It to analyze lane and band information only within that area Selecting the Area of Interest AOI 1 From the View Menu click on 1D Analysis and then select Area of Interest In the Image Window a white dashed rectangle appears within the image 2 Goto the 1D Analysis Menu and select Edit 1D Objects This allows you to manipulate 1D gel objects in the image 3 Posit
63. annotation by choosing Edit Annotations from the Tools menu then click on any part of the annotation 2 Press the DELETE key pi You can also select Delete from the Annotation Shortcut menu 67 Doc IT USER MANUAL CHAPTER ELEVEN VIEWING IMAGE INFORMATION Overview Calibrating Image Scale Image History Related topics OVERVIEW Doc lt keeps various sorts of information about an image This Image Information includes e Image Scale Described as the number of metric units in the image s width this information is used to calibrate Rulers and Measurement Annotations e Image Resolution The width and height of the image in pixels e Image Depth The number of bits used to represent intensity Doc It supports 8 bit and 16 bit image depth e Notes Anything you wish to enter about an image e File Properties The file name path create date and size All will be N A if the image has not yet been saved e Image History A list of material changes to the image when they occurred and any notes that you would like to add about why or how the change was made To be more compact the Image Information window is organized into two tabs All information except Image History is on the first tab Image History is on the second tab F lnaqge DTE STETIT E Xj Properties Hiuon mage Propet ta oma adi 5 arrpls th fia m Danmar ra Haroluhr Cd x TEE Ba Dashi Aba Hotes E File Piopa ia
64. aph Doc It displays an image of the graphed lane or of the lane you last selected to be graphed In this section the following topics are presented e How to display multiple lanes at one time e How to change variables for the x axis and the y axis and e How to change colors of the graph and how to display specifics such as band extents band peaks and background correction Ei You also can access the Lane Profile Graph using the 1D toolbar or using the context menu for Lanes or Bands Displaying Multiple Lanes Doc It allows you to display one or more lanes at a time 108 Doc IT USER MANUAL To Display a Single Lane Doc It has two options for displaying a single lane To Display a Single Lane by Selecting a Lane 1 Select Edit 1D Objects from the 1D Analysis Menu 2 Click on the lane you wish to see graphed 3 From the 1D Analysis Menu select Lane Profile Graph A new window appears with the lane you selected graphed To Display a Single Lane from the Lane Profile Graph 1 From the 1D Analysis Menu select Lane Profile Graph A new window appears with an empty graph 2 From the Lanes section to the right of the graph select the lane you wish to see graphed Doc lt automatically displays the graph of that lane To Display Multiple Lanes Doc It also has two options for displaying a single lane To Display Multiple Lanes by Selecting Lanes 1 Select Edit 1D Objects from the 1D Analysis Menu 2 Clic
65. apture Templates To Capture an Image Using the Advanced Capture Tab 1 If the Advanced Capture tab is not showing or if the Capture Panel itself is hidden choose Advanced Capture from the Acquire menu aie Doc IT USER MANUAL If another Capture Panel tab is showing you can also click the Advanced Capture tab at the bottom of the Capture Panel 2 Select the desired template from the drop down list To control all settings directly select Photo 3 If desired override the defaults for the selected template by choosing different values The template name and the control you alter will turn yellow to show that they are no longer at the default settings 4 Click Capture Camera Settings The Olympus camera supplies the following settings e Exposure Time The speed at which the shutter will be snapped Faster speeds mean less light enters the camera and the image will be darker but movement will be less blurry Slower speeds allow more light and result in brighter images but show increased blurriness if there is movement in the image being captured If the Exposure Time is set to Auto the camera will adjust it to match the aperture unless this is also Auto and the current lighting conditions e Aperture The degree to which the shutter will open The aperture setting is counter intuitive a small value indicates a wide aperture which allows more light to enter the camera and results in a brighter image and a la
66. apture tab before each capture hepa techn Tan pr O tsi aae A O Doc lt comes with a set of standard templates for use with various light sources To Create a New Template 1 On the Advanced Capture tab click Templates The Advanced Capture Templates window will appear 2 Click New The New Template window will appear If you don t have any capture templates yet the New Template window will appear automatically 3 Type a name for the new template and click OK A new template will be created and then defaulted to the current settings in the Advanced Capture Templates window 4 Set each camera setting to the desired value 5 Determine for each setting or group of settings whether you want to override the default before each capture If you do not want to override it select the Excluded Controls check box next to the setting or group of settings If you do want to override it clear the check box 6 Click Save or OK to save your new template pi To copy a template select the template you wish to copy first then click New The new template will use the one you selected for initial values To Edit a Template 1 Onthe Advanced Capture tab click Templates The Advanced Capture Templates window will appear 2 Select the template you wish to edit from the drop down list The default values and excluded controls check boxes will be set to the values used for that template 3 To edit the name click Edit Nam
67. are clear gaps between them It performs badly if bands in different lanes bleed together or touch because it will tend to eliminate almost all band data at such a point You also can access background correction using the 1D toolbar or directly on the Lane Profile Graph Viewing a Corrected Image To show you what the image would look like after background correction Doc It can create a corrected image This image is a new image similar to the results of Duplicate Image which retains all the current 1D objects but has intensities that have been adjusted per the selected background correction method To view a corrected image 1 From the 1D Analysis Menu select Background Correction and then select Corrected Image Doc It then changes the image to fit the corrections you selected Visually the image will appear darker or lighter if a white background image than before CONCENTRATION CALIBRATION Showing the Concentration Graph With the background of the image corrected Doc It now is ready to graph intensity versus concentration and to fit curves or lines on the graph Doc lt also allows you to change the Unit Type plotted on the y axis To Show the Concentration Graph 1 From the 1D Analysis Menu select Concentration and then Calibrate Concentration A new window entitled Calibrate Intensity appears with a blank graph 101 Doc IT USER MANUAL pi You also can access this feature using the 1D too
68. as soon as the weight is exactly on the band the color of the line changes from blue to yellow default colors This means you now have exact placement the weight will be exactly on the band peak Exact placement only occurs when the color changes from unmatched to matched further movement of the weight may alter the exact positioning When in doubt move the weight completely away from the band and reposition it with the arrow keys until the color changes mo On the second window of the calibration operation where you adjust weights to bands 5 you can change the colors of both the unmatched and the matched lines by using the controls in the upper right corner mo After Doc It calibrates two or more lanes Retardation factor lines will be automatically calculated and will replace any previous Rf line work 97 Doc IT USER MANUAL REMOVING A STANDARD FROM A LANE If you want to remove a standard from a lane do the following 1 From the 1D Analysis Menu select Lanes and then Calibrate Molecular Weight A new window appears 2 Choose the Back or lt button at the bottom of the window 3 Choose None from the Molecular Weights Standards list at the top of the list 4 Click OK Related Topics Chapter 14 Finding Lanes and Bands Chapter 17 Viewing and Printing 1D Gel Data 98 Doc IT USER MANUAL CHAPTER SIXTEEN USING THE 1D GEL TOOLS FOR CONCENTRATION CALCULATIONS Overview Background Correction
69. as well Note that you can only move a band between the bands next to it not beyond them 3 Click on OK The Lane Profile window closes and bands are now in their new positions 89 Doc IT USER MANUAL To Resize Bands To Resize Bands using the Image Window 1 Place the arrows over the band you wish to resize and click on the band Control handles will appear around the band 2 Place the cursor over the top or bottom of the band s box to increase or to decrease the height of the band Drag the top or bottom of the band until it is the size you wish it to be To Resize Bands Using the Lane Profile Graph 1 Under the 1D Analysis menu select Lane Profile Graph The graph appears in a new window 2 Ensure that Band Extents is selected Under the graph find the band markers Drag the markers to the left or the right to the place you desire them Note that the markers on the graph change position as well 3 Click on OK The Lane Profile Graph closes and the bands are now in their new positions To Place Bands Exactly 1 From the 1D Analysis menu select Edit 1D Objects 2 Select the band you wish to resize Control handles will appear around the band 3 Under the 1D Analysis Menu select Bands and then Band Properties The Band Information window appears 4 In the section of the window labeled Geometry you may change the numerical values of the top peak and bottom of the band 5 After you enter the new
70. at the bottom edge of the histogram right or left until the desired intensity range is marked Each time you release a marker the image will be intensity stretched using the current range Note that Manual will automatically be selected as soon as you move a marker OR Select Manual from options to the right of the histogram and type the range you desire into the From and To text boxes Click Apply To Turn Off Intensity Stretching 1 Ifthe image is not the foremost image select it from the Windows menu or click on its title bar See Image Windows for more information 2 From the Image menu choose Intensity Histogram You can also display the Intensity Histogram window using the toolbar or the pi shortcut menu on the Image window itself 3 Select None from the options to the right of the histogram INSIDE A PIXEL A computer image is made up of a rectangular grid of dots called pixels Each pixel is a single color bright red dark blue etc In a monochrome image each pixel is a shade of gray light gray dark gray black the ultimate in dark gray etc Internally the shade is represented by some number of intensity values Monochrome and Color Pixel Mechanics Monochrome images are fairly simple A monochrome pixel has a single intensity value ranging between 0 black and some maximum intensity which is white the ultimate in light gray Colored images are slightly more complex Computer color images t
71. ation e Rectangle Rectangle annotations allow you to draw a rectangular frame around part of the image You can use them to show the boundaries of an image feature You can select the color line thickness and line style solid dotted or dashed of a Rectangle annotation e Ellipse Ellipse annotations are very similar to Rectangle annotations except that they are oval rather than rectangular You can select the color line thickness and line style solid dotted or dashed of an Ellipse annotation e Highlighter Highlighter annotations work like a highlighting pen by altering the color of the underlying image to draw attention to an area You can select the color of a Highlighter annotation e Length Measure Length Measure annotations look somewhat like Line annotations except that they show the length of the line in image scale units see Rulers You can position Length Measure annotations from one point to another point to see how long any image feature is in real units You can select the color line thickness line style solid dotted or dashed font size and formatting bold italic or underline of a Length Measure annotation e Angle Measure Angle Measure annotations consist of three points They display the angle between the line formed by the first and second points and the line formed by the second and third points You can use Angle Measure annotations to determine slants in lanes or in related bands across lanes in an elec
72. be seen under a microscope with various kinds of lighting primarily for comparison purposes 2 To highlight specific intensities for analysis purposes For example one of the pseudocolor spectrums highlights black intensity 0 pixels with blue and white maximum intensity pixels with red This identifies the undersaturated and oversaturated parts of the image Doc lt supplies 19 built in pseudocolor spectrums e Over Undersaturation Colors black undersaturated pixels blue and white oversaturated pixels red e Ethidium Bromide Mimics the colors used in Ethidium Bromide gel preparation e Fluorescein Mimics the colors used in Fluorescein gel preparation e Green Fluorescent Protein Mimics the colors used in green fluorescent protein gel preparation e Texas Red Mimics the colors that appear with a Texas Red stain e SYBR Gold Mimics the colors that appear with a SYBR Gold stain e SYBR Green Mimics the colors that appear with a SYBR Green stain e SYPRO Orange Mimics the colors that appear with a SYPRO Orange stain e SYPRO Red Mimics the colors that appear with a SYPRO Red stain e Coomassie Blue Mimics the colors that appear with a Coomassie Blue stain e Silver Mimics the colors that appear with a Silver stain e Blue to Red Colors all intensities from blue at the low end to red at the high end using a natural light spectrum e Red to Blue Colors all intensities from red at the low end to blue at the high end
73. ber range from 0 to 65535 For a more detailed explanation see Inside a Pixel Intensity The measure of brightness of a pixel In a monochrome image each pixel has a single intensity In a colored image each pixel has three intensities one for red one for green and one for blue The actual intensity values depend on an image s depth JPEG A common lossy compression image format used to store images on disk JPEG files generally have JPG or JPEG extensions Lossless Compression Compression schemes that preserve the image s integrity in full Generally lossless compression results in much larger files than lossy compression on the same image Lossy Compression Compression schemes that tolerate some pixel value changes to make the 122 Doc IT USER MANUAL image compress to a smaller size Because the changes are irreversible the image has lost some of its original detail after such an operation Macro Mode Close up mode for a digital camera or web camera Macro mode is usually appropriate for imaging microbiology slides Microbiology The branch of biology dealing with microscopic forms of life Microscopy The use of or investigation with a microscope Monochrome Black and white with shades of gray Doc It cameras capture 256 shades of gray in monochrome mode Pixel Short for picture element A pixel is a single dot in a computer image The dot has a certain color for a color image or an intensity for a mon
74. c eed etre 42 Iisdem A A DM CDU DUREE 42 Monochrome and Color Pixel Mechanics cooocccocccnccccnnccccnnncncnncnncnccncnnonnnncnnnnnononnnnnananonos 42 The Meaning of Image Deplli caian id ta etu bota eheu Dad iat Anta la ausu Eus 42 DISPlayina Depas A aa Badenanet 43 Depths Greater than 8 bit in Doc It ooooocccoccnnccccnccccnncconnnocanononanononanonononononnnononnnnnanononos 43 CHAPTER EIGHT EFFECTS urnas 44 O mM 44 To Change Brightness Contrast Gamma Or INVert ooccccccccccocnncccnnnoconnnonnnnnnnoncconononononos 45 TO REUMO DESTUN Valtles s tube idum deed d bet me suut uia Pet dum Um Mud A UD OM EE 46 e 46 TOAD A PSelldOCOlOF xus tasto ic lion Diese diano puc Uso ied 47 TO REMOVE ASS UO COLON e a tercio dicas 47 ZOMIN ANd Pat cada 47 To Zoom Tho QUE uio dat to ted o ee ei 48 To Pan to a Different Part of the Image coccconccccccocnncoconnococoncnnonannnnnnannnnononcnnononnnnnnnanoss 48 CHAPTER NINE MANIPULATIONS 55 275 9a c25 c qu REo ias 49 SUI MN CENE 49 FS PCR ERE panied ceria 51 To Revert to the Last Saved Version occococccccccncccccncoccnnnconononannnnanononannnonannnonnnnononnnonannnnanenes 51 Duplicating Ima Si a Em 51 o Duplicate an Mage did 51 A 52 To Align the Image to a Feature cccconncccoccncconcnccconnccnonccnononononononnnnonanncnnnnnnnnnnnnnnnnnnannnenannnss 52 To Rotate an Image to a Desired Orientation oonc
75. ccccocccncoconcnnconononconanennononnnononrononnanennnnonons 53 To Rotate an Image by an Exact Number of Degrees ccoooccccoccccccccccoccnnccccnccnonocononononenononos 53 med AONZOMAl Y e is 54 TOFD alt mage Honzomally seen a a a a eaateacsate ante 54 RID Verica ruani o de arnes 54 PO FMD alr Image Verica e a n aa a a RM PLU EM a EM EAA 54 VSS DOCKS c 54 Doc IT USER MANUAL To Despeckle an Image ccccccccesececeseccceseccssecceeseeceaeceseueceusececeuecesaceesseseessaeeensueeensueseneaees o4 REMOVE NOS O e weenie 55 To Remove Noise from an Image ccccccocnncccocnncccoononoconcnnnnnacnnnnnnnnnnnnnnnnnnnnnnononnnnnnnnnnnnnnnnns 55 SPPE RAPERE mE 55 TOs Sharpe nan IMA italian 55 A o A E E sess tale Gress ddan ae ame 55 To Blan Made aaa os 55 EDOS S es fet ate NEU MU D DEM EE NIMM MANIL LI IMEEM ones 56 TOE MDOSS AMMA GS ETT ETT 57 e TERRE D UT TT etm of TOJdSSSIZe do MAS it dde ico tue tdm opis LE HIC TUERI NE E MEL PUE 58 A A IO QM 58 fom 83 co ok 2 pel g abe 10 Sacco rio oro NENT ee 58 Reduce TO MONO id A ia 58 To Reduce a Color Image to Monochrome c ooccccoccncccnncnncnnoconcnoncnnonnnconconanonnnnnncnnonnnnnnnnnncnnenanens 59 CHAPTER TEN ANNOTATIONS 545 3st ouscisa dues a a lise uec alo sa bee neu e ce P aue add 60 eI E 6
76. centration scale and unit Clear All Lane and Band Information Clears the image of all lane and band information leaving in place other annotations Data Explorer Displays data sheets with the calculated results from lane and band analysis such as Rf molecular weight and concentration values These values can also be exported to Excel for further analysis 1D Analysis Settings Opens up the Image Information Window There are also additions to the File menu and the View menu Additions to the File Menu Contains the same commands but with the following two additions Reports contains additional fixed reports specific to 1D Analysis data and Tabular Reports allows Data Explorer like values to be printed in a flexible report format Additions to the View Menu Contains the same commands with one addition the 1D Analysis submenu Under 1D Analysis from the View menu Doc It offers the following eight tools to control the display of 1D Gel data on the image Area of Interest AOI Displays a white serrated line appears on the image to mark the area involved in the 1D gel analysis Anything outside this area will be ignored by the 1D analysis routines By dragging its lines with the mouse you may select the exact area involved Lanes Identifies each lane in the image with a rectangle The rectangle will be in the specific color associated with each lane You can resize or reposition the lane by clicking inside the rectan
77. choose Duplicate Image A second copy of the image will appear in a new Image window ROTATE This manipulation allows you to rotate an image by an arbitrary number of degrees You might use it to correct for a misaligned gel The Rotate manipulation allows you to rotate the image easily by a graphically selected amount or to align the image based on an internal image feature A Huma lira py oem 14 note ane 342 w All instructions below assume the desired image is foremost If it is not select it from the 5 Windows menu or click its title bar To Align the Image to a Feature If the image has features that should be horizontal or vertical you can use the Align mode of the Rotate manipulation to rotate the image to correct alignment 1 From the Image menu choose Manipulation and then Rotate The Rotate window will appear and a grid will be overlaid on the image rm If the image has not yet been saved you will be prompted one time to save it E before the first manipulation you select 2 On the Rotate window select Align This should be the default 3 From a point on the image away from the center drag the grid around the center point until either a vertical line is aligned with the desired vertical 52 Doc IT USER MANUAL feature or a horizontal line is aligned with the desired horizontal feature The yellow arrow in the center indicates which way was up 0 degrees before you started dragging the grid
78. click Redo The last change will reappear run The Redo command will be unavailable if you have not yet used Undo O USING SELECTION TOOLS These tools allow you to mark part of the image for use in other operations Doc It has two selection tools Select Rectangle and Select Ellipse Select Rectangle selects rectangular regions Select Ellipse selects elliptical oval regions There are two operations in Doc It that use a selection region Copy and Crop Copy will copy the selected region to the clipboard If there is no selected region the entire image will be copied Crop will remove crop away all parts of the image outside of the selected region Either operation will work with either selection tool To Select a Region 1 Choose the desired selection tool Select Rectangle or Select Ellipse from the Tools menu 2 Starting with the upper left corner of the desired region drag the mouse downward and to the right until the desired area is marked You can actually begin at any corner You must end at the corner opposite to where you started To Adjust the Selection If the selection is not quite right you can move it or resize it without having to start over 1 To move the selection Drag the interior of the selection to the new location 2 Tomake the selection wider or narrower Drag the left or right dotted lines that bind the selection to the desired size 233 Doc IT USER MANUAL 3 To make the s
79. dit Annotations This step is unnecessary if you just finished adding an annotation Click on any part of the annotation Control handles will appear to mark the selected annotation If there are several annotations in the same area click on a portion of the annotation you wish to reformat that does not intersect any other annotation The control handles will show you if you have the wrong one The cursor will change from an arrow to a hand when you are over an annotation MOVING AND RESIZING ANNOTATIONS Once you have selected an annotation you easily can move it and resize it with the mouse To Move an Existing Annotation 1 Select the annotation by choosing Edit Annotations from the Tools menu then click on any part of the annotation pi If the annotation is not near any other annotations you can drag its interior immediately You do not need to select it first 2 Dragging from the interior of the annotation move it to the new position To Change the Points of an Existing Line Length Measure or Angle Measure Annotation 1 Select the annotation as described above 2 Drag the control handle for the point you wish to change to the new position The annotation will stretch appropriately as you drag To Resize an Existing Rectangle Ellipse Highlighter or Area Measure Annotation 1 Select the annotation as described above 2 Draga control handle inward or outward to define the new size The point on the opposit
80. dow The rulers show the width and height of the visible portion of the image either in metric units if calibrated or in pixels if uncalibrated Images captured through the camera and Darkroom Hood are calibrated automatically in centimeters As you zoom in or out and pan around the image Doc It updates the rulers to show the actual size and position of the visible portion of the image As you move the mouse over the image markers show your position on each ruler The units the rulers use are shown in the upper left corner see the image above Pixels uncalibrated are abbreviated px all other values use metric standard abbreviations When the rulers are calibrated to a metric measure they may change units as you zoom in For example an image calibrated in centimeters may switch to millimeters when you zoom in by a large percentage The measurements are still completely accurate the rulers switch units because they are designed to show you a useful number of units at every point The camera is calibrated at the UVP factory at a set distance from the camera to the gel surface However if the camera is used outside the darkroom the distance from camera to gel is changed or if the image comes from another source such as a scanner the image may not be calibrated or will be calibrated incorrectly and the image ruler may need to be recalibrated If this is the case the scale for the image can be adjusted through Image Information on th
81. e View menu 38 Doc IT USER MANUAL The scale information used by the rulers also is used by measurement annotations Length measure annotations can be used to see the length of a feature that is not square to the rulers To Show or Hide the Rulers You can show or hide rulers individually for each Image window Hiding the rulers provides slightly more space in which to view the image 1 Onthe View menu choose View Rulers pi This command is also available on the toolbar MAGNIFY TOOL This tool is a quick way to expand parts of the image without having to zoom and pan To Use the Magnify Tool 1 On the Tools menu choose Magnify 2 Position the mouse over the feature you wish to magnify and then click the mouse button You can also drag the mouse across the image magnifying as you go There is no need to turn off the Magnify tool it will be turned off automatically by selecting any other tool such as a selection tool or an annotation tool INTENSITY HISTOGRAM The Intensity Histogram shows the distribution of intensities in the foremost image This graph can be used to see which intensities actually appear in an image A tight group of intensities may represent an image that was either underexposed or overexposed or that has a large block of pixels with very similar intensities 39 Doc IT USER MANUAL For a much more in depth look at how intensities work and how the computer represents
82. e corner will remain fixed and the annotation will resize as you drag To Rotate a Text Annotation 1 Select the annotation as described above 2 Drag any control point around the center of the annotation until you reach the desired rotation pi If you have a hard time aligning the text exactly as you want it move the mouse away from the center of the text annotation while dragging 65 Doc IT USER MANUAL FORMATTING ANNOTATIONS The Formatting menu contains options to format a selected annotation You can use the menu in two ways 1 When you have selected an annotation tool to create a new annotation but before you place the new annotation you can set formatting options with the menu The options you select will appear on the new annotation 2 When you are using the Edit Annotations tool and have selected an annotation you can change its formatting with the menu The Formatting menu contains the following formatting options e Color You can either pick a color from the list or choose Custom Color at the bottom to pick any existing color All annotation types support color options e Line Style You can pick from solid dashed or dotted Only the following line annotations support line style Line Rectangle Ellipse Length Measure Angle Measure and Area Measure e Line Thickness You can pick a line thickness from the offered choices You can only select Line Thickness if the line style is Solid Otherwise
83. e for the First Time Camera hardware setup should be done prior to attaching the camera to the computer or installing driver software 1 Insert the battery packs included in the package into the camera See page 29 of the camera manual for illustrated instructions 2 Attach the camera AC power cord and plug it into an appropriate power outlet See page 33 of the camera manual for illustrated instructions 3 Insert the camera s Smart Media Card See page 35 of the camera manual for illustrated instructions 4 Initialize the camera for PC communication by turning on the Camera Control feature a Make sure the camera is not yet connected to the computer b Setthe camera mode dial on top of the camera to A S M C Open the Smart Media Cover do not remove the Smart Media Card just open the cover The camera display will show a message stating that the card cover is open d Press and hold the Menu and Monitor buttons for over three seconds The buttons are located on the back of the camera to the right of the monitor see page 24 of the camera manual for a diagram of camera controls The camera display will show the Camera Control menu options and its current state On or Off e Use the camera navigation controls to set the menu option to On and then press the OK button to the right of the monitor Doc IT USER MANUAL f Close the Smart Media Cover g Turn the camera off To Connect the Camera to the Co
84. e in a sensitivity value in the text box next to the Lane Sensitivity slider 5 You may also adjust the band sensitivity in the same manner as the lane sensitivity However it is usually premature to adjust band sensitivity if lanes are not correctly detected 6 Click Search at the bottom of the window to search the image using the parameters you specified 7 Right above the Search OK and Cancel buttons you will see how many lanes and bands Doc It found Your image now reflects these lanes and bands with colored lines and rectangles pi While searching for lanes you can adjust the Area of Interest and move or resize lanes without closing the Lanes Bands dialog Simply drag lines or corners to resize and object Drag the interior of a lane away from any bands it may contain to reposition it To Return to the Automatically Detected Parameters After changing lane and band sensitivity values you may wish to return to the values selected originally by Doc It for the Basic Search To return to the automatically detected parameters 1 Onthe Lanes Bands window click Set Parameters Automatically The original parameters will be restored and the image will display lanes and bands as originally detected in Basic Search If the search mode is Bands Only the lane sensitivity value will be reset but the system will not search for lanes with the new value To search for lanes and bands both ensure that the search mode at the top o
85. e to the right of the template drop down list Type a new name and then click OK 4 f you made changes in the Advanced Capture tab to the same template you are e Doc IT USER MANUAL editing you can make the template take the changed settings by clicking Sync This allows you to experiment with changes to settings and then save those changes 5 To change any setting default select the new value for that setting 6 Toexclude or to show a setting or a group of settings select or clear the related Excluded Controls check box 7 Click Save or OK to save your changes To Delete a Template 1 On the Advanced Capture tab click Templates The Advanced Capture Templates window will appear 2 Select the template to be deleted from the drop down list 3 Click Delete 4 Confirm that you wish to delete this template by clicking Yes You can make many template changes at one time by using Save instead of OK OK will close the Advanced Capture Templates window saving your latest changes SCANNING IMAGES Doc It can acquire images from scanners that supply a TWAIN interface Almost all scanners support TWAIN TWAIN allows Doc It to use the scanner s own software interface during scanning To Select the Desired Scanner 1 Choose Select Scanner from the Acquire menu The Select Source window will appear 2 Select the desired device from the list 3 Click Select The device you select will remain the d
86. ears when you edit a Text annotation which you can do by double clicking the Text annotation or by choosing Edit from the shortcut menu associated with it In order to speed up your work the Text Edit window saves the last text you entered making it the default for the next Text annotation you create To enter new text simply start typing and the existing text will be replaced You can enter multiple lines of text as a text annotation To have the text automatically word wrapped paragraph style select the Word Wrap check box To control when a new line is created manually clear the check box To Edit the Text of a Text Annotation Double click the Text annotation 1 ion 2 Inthe Text Edit window make any changes to text 3 Click OK SELECTING ANNOTATIONS After you have created an annotation you can select it either to change formatting properties or to graphically move stretch or resize it Since selecting and editing an annotation are different from selecting part of the image there is a specific tool the Edit Annotations tool that you use to select and edit annotations Every time you add an annotation the tool switches to the Edit Annotations tool automatically so that you can immediately edit the new annotation pi You can customize the Tools toolbar to include the Edit Annotations tool 64 Doc IT USER MANUAL To Select an Existing Annotation From the Tools menu choose E
87. efault until it is changed even after rebooting Generally if you have only one TWAIN device it will already be the default To Scan an Image from a Scanner 1 Select Scan from the Acquire menu 2 Change any settings offered by the device as desired Consult Help for the scanner to learn about the Scan dialog window for your device 3 Click Scan this button may have different names including OK or Acquire for different devices The image will appear in a new Image window in Doc lt Most scanners offer a fast preview mode You can use this to adjust brightness contrast and other settings appropriately before scanning 97 Doc IT USER MANUAL Related Topics Chapter 1 Moving Files from the SmartMedia Card Chapter 1 Setting Up the Camera Chapter 3 Image Windows Chapter 5 Loading Images Chapter 5 Saving Images Chapter 7 Rulers Chapter 8 Effects Tab 28 Doc IT USER MANUAL CHAPTER FIVE LOADING AND SAVING IMAGES Loading Images Saving Images Image Files Related Topics LOADING IMAGES Doc It will load images in most popular formats including JPEG TIFF GIF PNG TGA and BMP If the image was previously saved in Doc lt other image details such as the image s scale history and annotations will be loaded as well Eight demo images are included with Doc It so that you can experiment with different types of realistic images For a discussion of exactly how image information is s
88. election taller or shorter Drag the top or bottom dotted lines that bind the selection to the desired size 4 To change both height and width at one time Drag any corner control point to the desired size To Cancel the Selection 1 Click once anywhere on the image away from the current selection The selection markers will disappear m You can also cancel a selection by pressing the ESC key CoPY Used on an image the Copy command copies all or part of the image to the clipboard If the image currently has a selected region only that region is copied If the image currently has no selection the entire image will be copied mo Copy can also be used on text in which case it acts in the standard Windows fashion O Once an image or part of an image has been copied you can paste it into other software packages that support images You can also paste the clipboard contents back into Doc It using either the Paste or Paste Special commands Images pasted into other software packages will use the display settings from the Effects tab brightness contrast gamma invert and pseudocolor They will include annotations if the annotations were displayed when Copy was used If annotations were hidden they will not be included Images copied from Doc It and then pasted back into Doc It using either Paste or Paste Special will always include annotations and will be affected by display settings only on a temporary basis just like all
89. emoved by creating a frequency space mapping Fourier transform of an image and removing frequency spikes away from the graph s origin There are two issues to be aware of with noise removal First if your image has actual desired pattern information the operation will not be able tell these from noise and it will remove them second the mathematics of the operation can cause some edges pixels to be identified as patterns resulting in blurring on some images To Remove Noise from an Image 1 Ifthe image is not the foremost image select it from the Windows menu or click its title bar 2 From the Image menu choose Manipulation and then Remove Noise Removing noise a large image may take ten or fifteen seconds rm If the image has not yet been saved you will be prompted one time to save it E before the first manipulation you select SHARPEN This manipulation enhances edges in an image making them more visible It is easier to see fine detail after an image has been sharpened To Sharpen an Image 1 Ifthe image is not the foremost image select it from the Windows menu or click its title bar 2 From the Image menu choose Manipulation and then Sharpen Sharpening a large image may take a few seconds mo If the image has not yet been saved you will be prompted one time to save it 5 before the first manipulation you select BLUR This manipulation blurs edges in an image making them more less prominent You can
90. ent to hide them so you can see the other 1D objects more easily From the View menu select 1D Analysis then turn off Rf Lines Adding Rf Lines Manually ET x Doc It allows you to add Rf lines to an image with less than two lanes that are calibrated to molecular weight standards On images with two or more calibrated lanes Rf lines are created automatically and Doc It will not allow you to add new ones although you can adjust the automatically added ones as described in the Automatic Rf Line Determination topic To add an Rf line manually On the 1D Analysis Menu click on Retardation factor Rf Lines then Add Rf Line Rf lines will be made visible if they were formerly hidden and a window will pop up entitled Add Rf Line The cursor will now appear as a square cross and you can select the first band that is part of the Rf relationship Then click on a second and subsequent bands in other different lanes You may click on as many bands as you like to draw the line up to one per lane but note you must choose at least two and you can only choose one band in each lane To place an Rf line anchor circle on a non band location hold down the CONTROL CTRL key as you place the circles When you are finished selecting the points that will make up the line click Add Rf Line in the Add Rf Line dialog window The green line will now appear white and you have created a new Rf Line To place more Rf lines follow the same proc
91. ered in the Image Information window History Report Prints the image history as reported in the Image Information window Image and Properties Report Prints the image on the upper half of the page and the properties on the lower half Image and Effect Settings Report Prints the image on the upper half of the page and the setting values from the Effects tab on the lower half Image and Notes Reports Prints the image on the upper half of the page and the image notes on the lower half of the page and succeeding pages if required Image and History Reports Prints the image on the upper half of the page and the image history on the lower half of the page and succeeding pages if required All Image Information Prints the image on the upper half of the first page followed by the image properties effect settings image notes and image history on the lower half of the first page and succeeding pages as required All eight reports include a header and footer that you can set as you desire 212 Doc IT USER MANUAL z Dius icc 4 io Fiir es Formoe Edy Oh Dept E Dor ali Darren WA PE ee hi Bee al Pete AAA ee ere Y Cosa 1012000 91 20 2 PME ee ET SE 714 DEZ Pen d Whenever you request a report you will be shown a preview of the report as it will look The Report Preview window also allows you to adjust the header footer and margins so you can get the report you want To View and Print a Repo
92. ess Note however that you only will be able to place Rf lines as long as they do not cross another Rf line If you can place the Rf line the line will appear green If there are any red marks at all on the Rf line you create you will not be able to create the Rf line when you click 93 Doc IT USER MANUAL Add Rf Line Ensure that the entire line is green before clicking Add Rf Line 5 Click Close when you are finished adding Rf lines Moving Rf Lines You can adjust existing Rf lines whether they were created automatically or manually To move Rf lines to match bands of the same molecular weight 1 From the Analysis 1D menu select Edit 1D Objects 2 IfRflines are not visible turn them on through the View menu From the View menu select 1D Analysis then turn on Rf Lines 3 Select the Rf line you wish to adjust Control handles will appear 4 Anylane that has a white control handle without an X is an uncalibrated lane and it is possible to move the intercept point up or down by dragging it If the lane has a gray control handle with an X it is already calibrated and cannot be moved 5 After you have adjusted Rf lines you may find it convenient to hide them so you can see the other 1D objects more easily From the View menu select 1D Analysis then turn off Rf Lines Deleting Rf Lines Hf lines that were added manually can also be removed automatic Rf lines cannot be removed To Remove One Rf Line
93. etardation factor Rf or Molecular Weight MW to be displayed on the x axis then the graph takes into account Rf effects This means that other lanes may appear to be stretched or compressed horizontally relative to the selected lane If you select Concentration to be displayed on the y axis then the curve adjusts the intensities of the lane and relative differences in the graph may change Display Options In the Lane Profile graph Doc It allows you to choose what details you would like to see in the graph The program also allows you to change the colors of the background of the graph and of Its axes Display Options for Details Underneath the graph and the lane image in the Display options section you can select to view various details The following are available e Band Peaks Selecting this option means Doc It will display an arrow labeled with the band s position at the top of the band on the graph and a small rectangular control under the graph that can be used to move the band peak e Band Extents Selecting this option means Doc lt will display parentheses showing the width of each band and two small rectangular controls under the graph that can be used to adjust the band s extent e Corrected Values f you have asked Doc It to perform a background correction selecting this option means Doc It will change the graph to reflect the new values after the correction e Background Correction f you have asked Doc lt to per
94. euInGgSs On E a oi 79 CHAPTER FOURTEEN 1D GEL ANALYSIS FEATURES ooooccccccoococcnccnnnonncnnnnnonanennnnannnnenrnannnrrrnenananes 80 SIS 80 were e 80 DS IgM PRIN 80 AA or gute E ARUM TELE RENAL CR RERHE ERN READ RIAPEEE CAD SERE TNDU HERMES 82 1D Gel Image Window Features 2 ii a o aa Ye Oda Era Doa 83 1D Gel Preference MP e 84 11001 epe m 85 Finding 1D Gel Lanes and Bands ccoocccccnccccncccnccncncncncconnnnnnnonnnonnnnnnnnnnnnonnnnnnnnonnnnnnnnss 86 Identifying Area of Interest ocooonnnccccnnnncccncnococonnnoconconnnnannncononcnnnnnnrnnnnnannnonannnnonnnnnnnnnananss 86 Searching Tor Lanes and Bands ui e 87 MOGIIVING BANGS rana iaa 89 Adding Bands Manta ida 89 MOVING and RESIZING Bandas uineis ata E E Rated uenit E ina 89 Deleng BANOS RT 90 Clearing All Lane and Band Information oocccoccccccncoccccncnccnnicncncnonnnnnnnnoncnncnnonnnnnnonos 90 To Clear All Lane and Band NTOnmMatlOn ci tita tro aaa one I M NO d Poe h Duos ade 90 Doc IT USER MANUAL CHAPTER FIFTEEN USING THE ID GEL TOOLS FOR MOLECULAR WEIGHT CALCULATIONS 92 OVNIS do 92 Retardation Taetor UNS a a ET 92 Automate R Eine Determinat oN zeinena Ad 92 Molecular Welght Calli AON sets e dd 94 Managing Weight Standards occcoonncncoccncnncconcnnconconconononnnnnnnoncnnncnnnnnnrnnnnnnrnnnonnnrnonnnrnnnnnaninnss
95. f the window is Lanes and Bands Searching Existing Lanes for Bands Doc It allows you to make band searching more or less sensitive resulting in more or fewer bands detected To Search for Bands in a Lane 1 From the 1D Gel Menu click on Find Lanes and Bands 2 Ensure that the search mode at the top of the window is for Bands Only 3 You may now choose the sensitivity for bands The fewer the bands that you want the farther to the right you will drag the slider To find more bands move the slider to the left 4 Then click on Search at the bottom of the window Right above the Search OK and Cancel buttons you will see how many bands Doc It found Your image now reflects the new information You can also use the toolbar or right click on a lane and select Search Bands in Lane This alternate approach allows you to pick individual lanes in which to search for more or fewer bands 88 Doc IT USER MANUAL MODIFYING BANDS If Doc It did not find all the bands in a lane you can add bands manually Just as with lanes you can also move resize and delete bands In this section you will learn how to do so Adding Bands Manually Doc It allows you to add bands manually To Add Bands Manually 1 Onthe 1D Analysis Menu click on Bands Select Add Band 2 Move the cursor over the image A movable horizontal line will appear whenever you move the cursor over a lane Simply move the mouse over the image to the spot
96. flickering the flash prior to the shot The flash should always be off when in the hood so this setting is only used when taking pictures with the camera outside the hood e Color Capture Determines whether the camera captures in color or monochrome e Image Quality Consists of Resolution and Compression e Resolution The number of pixels captured by the camera Larger numbers of pixels higher resolution result in a superior image with greater detail but also take more disk space e Compression The degree to which images will be compressed and the tolerance for small non visible changes to the pixel values known as loss High compression values result in smaller disk space usage but in greater loss Low compression 24 Doc IT USER MANUAL values result in larger disk space usage often much larger but in higher image fidelity e Optical Zoom Sample Size The zoom setting of the camera s lens Higher zoom settings make the subject appear closer but cover a smaller area Because the Doc lt hood has a fixed height the area that will be snapped at a given camera zoom setting can be known in advance This allows the system to show you the largest sample size that will be completely captured at a given optical zoom setting This same information is also used to calibrate the image rulers Sample size cannot be known if the camera is not at a fixed distance from the subject i e if the camera is not in the hood and should be ig
97. form a background correction selecting this option means Doc It also will place on the original graph the graphed line of whatever background correction you chose rn If you have chosen a background correction you can display either the graph with corrected values or 5 the original graph with the correction line It is not possible to display both at once Color Options Depending on what color the lane lines are you may wish to change the background color of the graph for easier viewing To do so 1 Underneath the Lanes options in Lane Profile Graph click on the down arrow of Background Color 2 Select the color you wish to see Doc It automatically changes the color Doc lt also allows you to choose the color of the graph s axes To do so 1 Underneath the Lanes options in Lane Profile Graph click on the down arrow of Axis Color 110 Doc IT USER MANUAL 2 Select the color you wish to see Doc lt automatically changes the color Background Correction Options If you wish to change the background correction option from the Lane Profile Graph 1 Underneath the Lanes options in Lane Profile Graph click on the down arrow of Background Correction 2 Select the correction you wish to see Doc It automatically changes the graph Note that the fourth option under Display also reflects the correction change You can choose whether to show or hide the background correction by selecting this box You can also select t
98. formation Lind ol uz ru Line Hares fF Lae bdh it coralani across ali lar Fe Fore al nes sraigh hz Th law aburra le thet sun of all ds barda Font Sine Lane Font Sie Bant 8 Image Eignir cobol m Black Frida C Unknown Esci gecumd Lonechbon m Hora Fl Shagi Lra C JoredVales C Ama Essen Lanat Aoling Dee DicRadur a Three major tabs are available two are History and Properties which are the same as before and third 1D Gel tab appears This tab allows you to perform the following functions e Unit of Mass This feature is for concentration units The unit of mass that appears is ng or nanograms Note that by clicking on Unit Names you may add further units of 85 Doc IT USER MANUAL your own Mass numbers are units of weight copy numbers relative units or any relational units you define e Lanes Use this command to make lane width constant across all lanes to force all lanes straight and to make the lane volume the sum of all of its bands as opposed to all intensities that fall within the lane area e Font size By clicking the buttons for Font Size Lane and Font Size Band you may choose the font size for the Lane ID Lane Name and Band ID labels The font range is from 6 20 e Image Background Color This indicates whether the background of the image is black white or unknown If you tell the system that the background is a color it is not however It will be unable to find l
99. ft side and lighted on the right side Horizontal lines would become harder to make out 56 Doc IT USER MANUAL To Emboss an Image 1 Ifthe image is not the foremost image select it from the Windows menu or click its title bar 2 From the Image menu choose Manipulation and then Emboss The Emboss window will appear cun If the image has not yet been saved you will be prompted one time to save it E before the first manipulation you select 3 Select the desired Emboss Direction The Preview window will show a thumbnail sample of what your image would look like embossed from this direction You can use the arrow keys to cycle through all eight directions while watching the Preview 4 Click OK Embossing a large image may take a few seconds RESIZE The Resize manipulation allows the image to be changed in size lt replicates or merges pixels as appropriate to arrive at the new size Resize most commonly would be used to create a smaller version of a very large image to allow you to increase response time during manipulations or to import the image into another software package that does not accept large images gt There is little point to increasing an image s size although the manipulation does support it Such an image would have more physical pixels after the operation but it does not gain any new information content 57 Doc IT USER MANUAL Cutt Aut THA x TR Nene resp n For Sales Dessed Si
100. ge the portion of the image that is visible easily by Panning The Zoom and Pan controls are located on the lower part of the Effects tab The current zoom factor for an image also is shown in the Image window caption AT Doc IT USER MANUAL To Zoom In or Out 1 If the image is not the foremost image select it from the Windows menu or click on its title bar 2 Ifthe Capture Panel is not showing or is showing a tab other than the Effects tab choose Effects from the Image menu pi You can also show the Effects tab from the toolbar 3 Click on Zoom In or Zoom Out located below the thumbnail version of the image on the Effects tab on either side of the slider OR Slide the zoom slider same location to the left to zoom out or to the right to zoom in OR Select the desired zoom factor from the drop down list to the right of the slider and buttons You can also type a number into the drop down box and press TAB This is particularly useful if you desire a zoom factor between choices in the list To Pan to a Different Part of the Image 1 Ifthe image is not the foremost image select it from the Windows menu or click on its title bar 2 Ifthe Capture Panel is not showing or is showing a tab other than the Effects tab choose Effects from the Image menu pi You can also show the Effects tab from the toolbar 3 In the thumbnail image drag the Pan rectangle to the desired location If the desired l
101. gle or on its edges Lane ID Identifies lanes with the lane ID Lane IDs are letter codes starting from A Lane Name Displays the specific names for each lane that you entered in Lane Information if any Bands Displays shows horizontal band lines at the band peak within each lane You can resize or reposition a band by clicking on its band line and then dragging the control handles that appear Band ID Labels each band with the letter of its lane and the number of its placement e g A4 Lane Curve Lines Displays lane curve lines which are single vertical lines down the center of the lane You can curve the lane in any fashion by dragging the line left or right 81 Doc IT USER MANUAL e RF Lines Displays Retardation factor RF lines in the image One fixed RF line the zero line always appears at the top of all lanes Depending on the analysis there may be other RF lines Lines other than the zero line can be adjusted by clicking on them and dragging white control handles up or down grey control handles with X across them are established by molecular weight calibration and cannot be moved gt Some commands have accelerator keys CTRL something that allow you to access the commands more quickly Virtually all commands can be placed on the toolbar through the Preferences window 1D Gel Toolbar Doc It toolbars allow you to select most commands with a single button click The toolbars are completely
102. he range will appear as white Pixel values inside the range will be scaled similarly values close to the lower end will be nearly black values in the middle will be of medium intensity and values at the upper end will be nearly white For a much more in depth look at how intensities work and at how the computer represents images internally see Inside a Pixel later in this chapter rane Micra j There are three options for intensity stretching e None No intensity stretch is done Pixels are displayed exactly as captured e Automatic An ideal intensity stretch range using statistical sampling of the image pixels is applied by Doc lt e Manual You select the range for the intensity stretch Intensity stretching takes place before any Effects tab features You can brighten change the contrast or gamma contrast of invert or pseudocolor an image whether you use intensity stretching or not Using intensity stretching does not alter the image in any way To Stretch Intensities 1 If the image is not the foremost image select it from the Windows menu or click on its title bar See Image Windows for more information 2 From the Image menu choose Intensity Histogram 41 Doc IT USER MANUAL You can also display the Intensity Histogram window using the toolbar or the pi shortcut menu on the Image window itself 3 Select Automatic from the options to the right of the histogram OR Drag the intensity markers
103. hide all annotations on an image with a single command Each Image window keeps track of whether the annotations are hidden or shown for that image So you can show annotations on one image while hiding them on another image Annotations are shown automatically when you select any annotation tool so that you 5 can see what you re doing To Show or Hide Annotations for an Image 1 If the image is not the foremost image select it from the Windows menu or click its title bar 2 From the View menu choose View Annotations If this menu option is checked but no annotations appear you have not yet put any annotations on the image TYPES OF ANNOTATION Doc It offers eight different types of annotation e Text Text annotations consist of written information You can use them to label a particular part of an image You are able to select the font size color and formatting bold italic or underline of a Text annotation Text annotations display in a constant size no matter what the zoom factor is to ensure that you can always read them 61 Doc IT USER MANUAL e Line Line annotations permit you to draw lines with optional arrowheads at one or both ends You can use them to associate other annotations such as text with a particular image feature or to draw attention to an image feature You can select the color line thickness line style solid dotted or dashed and arrowheads none at start at end or both of a Line annot
104. i e the incoming image is copied entirely over the existing image wherever it lands Blend is used primarily to place comparison information into an existing image especially when using high proportions 35 Doc IT USER MANUAL Add adds pixels in the incoming image to those in the existing image up to maximum intensity Add is used primarily to build composite images with little or no overlap Subtract subtracts pixels in the incoming image from those in the existing image Subtract is used primarily to test for differences in or motion between two otherwise similar images Merging results in a new image that includes the existing image plus all of the area of the incoming image even if that area is off of the edge of the existing image This allows you to compose mosaic images usually with Add by placing the incoming image at the edge of the existing image To Merge Two Images 1 Place one of the images on the clipboard using the Copy command If desired a subregion of the image can be used See Copy for more details 2 From the Edit menu choose Paste Special The Paste Special window will appear pi Paste Special also is available from the Toolbar and the Image window s shortcut menu 3 Ifthe incoming image is large select the Preview Frame Only check box This will allow you to position the incoming image without the lag caused by redrawing a large image Otherwise clear the check box so that
105. idth of the scene in the image would be 1 m If you focused the shot so that exactly half of the ruler was visible from left to right the width of the scene would be 500 cm 1 2 m Display the Image Information for the image See Viewing Image Information for instructions In the Overall Sample Width area select the metric unit the right most drop down list first For example if the sample width of the image is 500 cm select centimeters Type the number of metric units in the text box immediately following Overall Sample Width For example if the sample width of the image is 500 cm type 500 4 Click OK IMAGE HISTORY Each material change to an image is tracked in Doc It s Image History feature Material changes include use of any Manipulations and use of the Paste Special feature Changes to Effects and Annotations are not tracked in the Image History Entries in the Image History may be of three types e Creation Describes how an image was created captured or scanned and provides some details e Change Describes use of a Manipulation or a Paste Special e Error Describes an error that occurred while reloading the image from a saved file The main use of an Error entry is to track the times when the image was changed in another software package which is important for some kinds of laboratory practice The Image History includes information on e What type of entry it is from among the types described ab
106. ilable through the Capture Panel If you hide the Capture Panel you can show it with commands on the View Acquire and Image menus whenever you need it e File Menu Contains commands to load and to save files to adjust preferences and to print reports a m um File Edt View Acguire Image Open Cirio Aiert Close Ctrl Fe Save Ctri 5 Save fe Report Prin Ctrl P Preferences Demo Images CHLIVPIDNA Color tit Exk ire 249 Doc IT USER MANUAL e Edit Menu Contains the Undo command and the four clipboard commands Cut Copy Paste and Paste Special Edit Yew Acquire Image Linda Ctrl 2 Redo Ct hr Copy Ctrl C Paste Ctrl Ctrl Paste Special e View Menu Contains commands that show and hide various main window features and commands that affect how the current sub window is displayed View Acquire Image Tools Fi View Toolbars w View Status Bar w View Capture Panel ctrl E View Annotations Ctri A w View Rulers Ctrl F Image Information CErl D Actual Size Fit To Window Ctrl F e Acquire Menu Contains commands to control a scanner and to show the Basic or Advanced Capture tabs of the Capture Panel Acquire Image Tools Form Earn Select Scanner Use Basie capture Use Advanced Capture BE ie S Doc IT USER MANUAL e Image Menu Contains commands that show the Intensity Histogram and the Effects tab of the Capture Panel and com
107. in the process Reusing one or a small number of Image windows is more efficient than generating a new one each time However images discarded in this fashion will be lost unless they were saved first and you cannot easily compare two images to see what you like and don t like with this check box selected con The Basic Capture tab has the following fixed settings e Aperture is 2 6 e Compression is Low e White Balance is Auto e Light Metering is Normal e Flash is Off e Focus Mode is Distance Auto Focus e Exposure Compensation is 0 LE Doc IT USER MANUAL Capture Templates e p Capture Templates are groups of preset camera Seed settings They are used on the Advanced Capture tab either to return the camera quickly to a group of das Hal La Perel pers mr Leer eae pee ae Esposas Tr fir im l settings that you use often or to default some c f ES H settings while making others available for Lado Blase n Tarda Come Ci alteration AA sa EU 1 Fah mei ra I i Cola Cpu f Dok Dor Cond Each template has a name a default value for e e gabe every camera setting and a list of flags indicating Comer E Sie which settings will be excluded and which will be A is shown from the Advanced Capture tab when this ES ek ES template is selected If a setting or group of 9 iurare E settings is not excluded it can be overridden on re SII owe the Advanced C
108. ion the mouse on the white dashed line to move that side of the AOI or at one of the corners to move that corner of the AOI Then drag the line or corner to where you would like it to be Drag any of the AOI corners to proportionally decrease or increase the size of the entire rectangle at one time 86 Doc IT USER MANUAL Searching for Lanes and Bands To Perform a Basic Search Search Made C Lanes and Bands Bands Only Options Force all lanes straight Search Parameters Image Background Black 7 White Lane Sensitivity More Lanes Fewer Lanes 1 127 Band Sensitivity More Bands Fewer Bands a I I 1 I I I 1 I I 1 1 uo Set Parameters Automatically r Lanes and Bands Found Lane Count T Band Count 38 w emen From the 1D Gel toolbar menu click on Find Lanes and Bands The Lanes Bands dialog window appears and a basic search using automatically determined parameters is performed If the results are not satisfactory you can keep the window open and adjust the search parameters as described in the following section or click OK and use the manual Add Lane and Add Band functions to identify all lanes and bands correctly Clicking Cancel returns the image to the state it was in before you opened the Lanes Bands dialog for instance if you had no lanes or bands before opening the window Cancel
109. it Types 2 Click on the unit name you wish to delete you cannot delete Concentration Then click on Delete Doc It removes the unit name 3 Click OK SELECTING DATA POINTS Once you have brought up the Concentration Graph Doc It asks you to select data points to plot on the graph 102 Doc IT USER MANUAL Selecting Data Points Dli sbb ate Intensity DAA Mona In the Calibrate Intensity Window note that there md are two tabs Graph and Data Points Selecting data points from either tab is substantially the same trame 1 Click on a band in the image that you A7 Dai Foris Graph wish to see graphed A new window C4 E E3 TEE entitled Add pops up The new window Custom lists the positions of bands in the image with the same Intensity if there are any if the band you chose is the only one with that intensity it is the only one listed gives the Intensity Value of the band and displays the Calculated Values of the band s listed To change the number in the Calculated Values section which corresponds to the Concentration point on the y axis simply type in whatever number you choose Click OK in the Add pop up The data point you selected is now plotted on the graph under the Graph tab Under the Data Points tab Doc It shows the exact position of the data points and where they will be plotted Select as many data points as you wish following the steps above Note that as you add in data
110. ition where the bright spot is somewhere in the middle of the image and where bands are sharply defined and quite distinct Rolling Disc Picture turning the lane profile graph upside and then rolling a ball over the new top Everything the ball is able to roll over is eliminated by Doc It Whatever the ball cannot fit into remains in the graph for your analysis Rolling disc performs well in all background conditions providing the size of the disc is carefully chosen An excessively small disc will roll into bands eliminating the band data almost entirely An excessively large disc rolls across the lowest valleys acting much like Straight Line correction 100 Doc IT USER MANUAL E To Use Rolling Disc l i 1 Select Rolling Disc from the Background a 5 ET Correction Menu under the 1D Analysis Menu Canel A pop up window appears asking you to set the size of the radius of the disc You can choose a radius size between 1 and 50 Change the size either by typing in the number you want or by using the up and down arrow signs to the right of the number box Click OK when you have the size you want Area Between Lanes Part of the image may be overexposed and there may be patterns of deformity between the lanes This correction takes cross sections between lanes and subtracts those inter lane profiles Area Between Lanes performs well in all variable illumination situations providing lanes are distinct and there
111. k on the lanes you wish to see graphed as you hold down the CONTROL key 3 From the 1D Analysis Menu select Lane Profile Graph A new window appears with the lanes you selected graphed To Display Multiple Lanes from the Lane Profile Graph 1 From the 1D Analysis Menu select Lane Profile Graph A new window appears with an empty graph 2 From the Lanes section to the right of the graph select the lanes you wish to see graphed Doc lt automatically displays the graphs of those lanes To Change the Selected Lane 1 Click on Lane in the graph 2 De select or re select the desired lane in the Lanes list Axis Options Depending upon what type of analysis you wish to perform you may change what variables appear on the lane profile graph s axes By default the x axis displays Pixels and the y axis displays Intensity However after calibrating molecular weight you may select to view Pixels Rf values or Molecular Weights MW Standard on the x axis Similarly after calibrating concentration you may select to view either either Concentration or Intensity on the y axis 109 Doc IT USER MANUAL To Change Axis Variables To change axis variables after you have performed either molecular weight calculations or concentration calibrations simply go to the Y Axis and X Axis options under the bottom left of the graph Select the variable you wish to see displayed Effects of Selecting Other Axis Values If you select R
112. l calibration data is removed and you can start a new analysis Changing the background correction method changes net intensity values and therefore invalidates concentration calibration Doc It will automatically ask you if you wish to remove all concentration data if you change the background correction method Answering Yes is the same as selecting Remove All Calibration Data Related Topic Chapter 17 Viewing and Printing 1D Gel Data 105 Doc IT USER MANUAL CHAPTER SEVENTEEN VIEWING AND PRINTING 1D GEL DATA Overview Lane Information Band Information Lane Profile Graph Data Explorer and Tabular Layouts Viewing Data in the Explorer Tabular Reports Export Data Fixed Reports Related topics OVERVIEW Doc It simplifies viewing and printing information about the image lanes bands and analyses In this chapter you will learn the following e How to view lane and band information e How to use the Lane Profile Graph including displaying multiple lanes in a graph changing the variables on the axes and changing the display options e Managing and printing tabular reports e Using the Data Explorer e Exporting data and e Viewing and printing fixed reports of analysis settings analysis lanes analysis bands and the lane profile LANE INFORMATION In Doc It you have several ways of viewing lane information e In the Lane Profile Graph e Inthe Data Explorer e In Tabular Reports e In Analysi
113. lane and band markings leaving only annotations Background Bkgr Correction Corrects the background with your choice of methods No Correction Straight Line Joined Valleys Rolling Disc and Area Between Lines Data Explorer Brings up datasheets showing the results of calculations on lanes and bands Analysis Settings Shows the 1D Gel tab of the Image Information window This tab shows the unit of mass lane and band fonts background color and whether the background 82 Doc IT USER MANUAL correction method in force if any e Edit Objects Allows you to select move and resize lanes bands Rf lines and the area of interest AOI How to Position the 1D Toolbar The 1D Gel Toolbar automatically aligns vertically to the left of the image window To change the placement of the Toolbar 1 Under the File Menu choose Preferences A new window appears 2 Click on the 1D Gel tab 3 Under View Options note the section on Align Analysis Toolbar Here you can select whether to align the toolbar at the Top Bottom Left or Right 4 In this tab you can also choose to display the captions along with the toolbar icon images 1D Gel Image Window Features In addition to displaying the image the Image Window also displays various 1D gel objects and allows you to manipulate them using the mouse The Image Window may display any or all of The Area of Interest AOI Lanes marked by colored rectangles Lane Cur
114. lar Report It is what the report will look like when you print it Deleting Tabular Layouts 1 Under the File Menu select Tabular Reports A new window entitled Tabular Layout appears 2 Select the name of the tabular report you wish to delete 3 Click Delete Doc lt erases the report Copying Tabular Layouts 1 Under the File Menu select Tabular Reports A new window entitled Tabular Layout appears 112 Doc IT USER MANUAL 2 Select the name of the tabular report you wish to copy 3 Click Copy Doc It automatically copies the report in the window entitling it Copy x Previewing Tabular Layouts 1 Under the File Menu select Tabular Reports A new window entitled Tabular Layout appears 2 To preview the report click Preview A new window appears that summarizes the data that will be included in the report Click OK 3 Another window appears entitled Analysis Tabular Report It is what the report will look like when you print it pi You also can access this feature using the 1D toolbar VIEWING DATA IN THE EXPLORER Aside from viewing graphs and information windows about the lanes and bands Doc It also offers you the option of seeing the data in a spreadsheet format 1 To access this function from the 1D Analysis Menu select Data Explorer A new window appears The Data Explorer has three tabs Analysis Lanes and Bands Under the Analysis tab you can find out the following e
115. launched from the Toolbar menu The name of the application you select will appear on the Toolbar menu After Capture Allows you to automatically rotate and flip each image immediately after capture if required The system also allows you to control whether to save implicit changes to indicated options above By default the system always saves these settings If you prefer to be asked whether to save changes each time you exit select Ask On Exit If you never want to save or if you have 76 Doc IT USER MANUAL set the options the way you want them to be select Keep Current Settings E user preterea A Options Toi fai Misa Tock 9 Vies Status Bar R Vien Captus Panel Ves Image Aukett F Dok Caput Pare Fight Use toolbar button caption v Un nem magas prompt ici rm bakna adorno slieratiora Magny Tool Lest 3 a Flecenty Mirad Fie List 7 5 Etemadi O Fed Bier Capture Fipimager Horzontally Fipimsgez Vertido Fiolale by lo Deyse Save Sena on Eat C T PET fe dk r Exit ssp Darsni Seine ar ae x To reset the Options to the application s original defaults click Factory Settings To Change Options 1 From the File menu choose Preferences The Preferences window will appear with the Options tab showing 2 Select and clear options as desired 3 To select an external program type the full path and filename of the program or click Find to browse for the program s EXE file on disk
116. lbar Changing Unit Type When you bring up the Calibration Graph the Unit Type plotted along the y axis is given as Concentration Selecting Unit Type If you wish to plot a different type of unit along the y axis do the following 1 Under the Unit Type menu above the graph click on the drop down menu 2 Select the unit type you wish to see displayed The y axis reflects the new unit name ro If you do not see the unit type you want in the drop down menu Doc It allows you to add it in See Adding a New Unit Type below Adding a New Unit Type If the desired unit name is not available do the following 1 Under the Unit Type menu above the graph click on the button to the right with three dots A new window pops up labelled Unit Types 2 Click on Add Another pop up window appears labelled Add Unit Name Under Unit type in the name of the unit you wish to see appear 3 Click OK Editing Unit Type 1 Under Unit Type menu above the graph click on the button to the right with three dots A new window pops up labelled Unit Types 2 Click on the unit name you wish to edit you cannot edit Concentration Then click on Edit Another pop up window appears labelled Add Unit Name Under Unit type in the name of the unit as you wish to see it changed 3 Click OK Deleting Unit Type 1 Under Unit Type to the right of the graph click on the button to the right with three dots A new window pops up labelled Un
117. mage width and cannot be changed There are two ways to set the image s scale 1 If you know the size of a single feature anywhere in the image you can use the Scale Tool to set the scale of the entire image from that one feature 2 If you know the size of the entire image in metric units you will find it easier to change the Sample Width through the Image Information window To Calibrate the Image Using the Scale Tool 1 If the image is not the foremost image select it from the Windows menu or click its title bar 2 From the Tools menu select Image Scale 3 Find the feature for which you know the metric size Click one edge of the feature 4 Move to the other edge of the feature As you move the mouse the scale tool will show you how many pixels you are marking with the tool 5 Click the other edge of the feature The Set Scale window will appear 6 Inthe Set Scale window select the metric unit for the marked area e g 69 Doc IT USER MANUAL centimeters and enter the number of units e g 12 7 Click OK The rulers will reflect the new scale To Change Sample Width for an Image Sample Width is calculated from the width of the image which in Doc It is usually an image of a sample or gel It is the metric distance of the width of the scene in the image For example if you removed the camera from the hood and carefully focused it on a 1 meter ruler fitting the ruler exactly from left to right the w
118. mands to manipulate the image Image Tools Formatting Window Help Intensity Histogram Effects Rotate Flip Horizontally Flip vertically Despeckle Sharpen Blur Emboss Resize Grop Reduce To Mono Manipulation Duplicate Image e Tools Menu Contains a list of the tools you can use to interact with an image including Selection tools the Magnify tool and Annotation tools Tools Formatting Window Hel Select Rectangle ShiFt F1 Select Ellipse Shift F2 Magnify Shift F3 Image Scale Edit Annotation Shift F6 Text Shift F Line Shift F8 Rectangle Ellipse Highlighter Length Measure Angle Measure Area Measure 14 Doc IT USER MANUAL Formatting Menu Contains selections to control the appearance of an annotation Formatting Window Help coor i Line Style k w Red Line Thickness k Green Arrow Style k Blue Yellow Fon Size F R Purple Bald GB Turquoise Italic CEFIH I Underline Chu e dering L Black Custom Color 1D Analysis Menu Contains commands to work with lanes and bands and to perform calculations in 1D Gel Analysis iD Analysis Window Help Lane Profile Graph Edit 10 Objects Find Lanes and Bands Lanes Bands Relative mobility AF Lines Background Correction Concentration Cw r F F F Clear All Lane Band Information Data Explorer 10 Analysis Settings Windows Menu Contains commands to organize Image windows Windo
119. me EU MEE M CRM EE AE M EE 104 CU OMZ e un dace cd Di ad LU E Uu REM LEE 75 OPIO NS tati aaa 76 o P P TR 75 TOODA tias 17 CUSTOMIZING Toolbars ii sida 17 Cut OI Edg8s dio 58 D Data E S T 80 82 113 115 116 Data POING es EP 102 Delia ai M 102 eligo adie 102 wedge e 102 Bis 90 BI ue g rte ET 82 Dele ind nabo a paid 102 UNI TDG ai Na dl dvd 102 BOC ERES 66 Bio assets shee te o 122 DESPERO see o4 Digi Doc It AICA A caro 11 A A Sede cece E THEE T SVS lent REGUN GMENS raene o a a a a a a aa 1 DISC irs ACS sion Siete E a a eel eee tent cukenaaedle 117 O 99 Bos tee Eee mn D eee ene ere ee E a encore 104 Draw Margin LINGS titer t busted tanta ntesbencsh a aA 115 117 118 119 120 Duplicate Mage sbaen 51 E EGIC WD ODiSGIS sisas 80 86 89 EGU IVS Taxes sico 12 EIU ODO CUS td a 82 E GMIN O Mert rEER 32 102 A a e HT AAEE 34 A A AE 35 Pate peca METTE 35 DS A A A O 102 ETIGCIS T A eee atatt Malte eine dial dero d NM cf p Male Lane DA eid uA 18 O oo dis dns EMI UM EE ME IU EINE RM ME 44 ConlbasE aie cs cates uec Mum Lui du nM 44 aamitideud eui ee uu dud Me d dua d EE 44 126 Doc IT USER MANUAL IB IRR 44 misizilo 0 90 0 MENTRE OT mmm
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121. mputer Only connect the camera to the computer while both the camera and the computer are off 1 Setthe camera mode dial to Off 2 Connect the camera USB cable to the camera USB connection port See page 198 of the camera manual for illustrated instructions 3 Connect the other end of the USB cable to the computer 4 Turn the camera on by selecting A S M on the mode dial To Install the Camera Driver Software Do not try to install camera driver software until Doc It has been installed the camera hardware has been set up and the camera is both connected to the computer and turned on 1 Turn on your computer leaving the installation CD in your CD ROM drive 2 When the Add New Hardware wizard appears click Next 3 Select Search for the Best Driver for Your Device then click Next 4 Select CD ROM drive then click Next 5 Follow instructions from the Wizard screens as they appear clicking Next Accept or Finish as appropriate 6 When the hardware installation is complete Doc It is ready to use To Insert the Camera into the Darkroom Hood Refer to the System Set Up and Installation Manual To Attach the Security Key The security key is a hardware device that attaches to the parallel port of your computer It unlocks Doc It s acquisition capabilities If you purchased the Doc It 1D Analysis module the security key will unlock the analysis menu functions Doc IT USER MANUAL Parallel Port Security Key
122. n intensity level decreasing it can make patterns that cross intensities more clear e Gamma Contrast also affects the difference between light and dark parts of the image but it does so by using a gamma correction curve The gamma correction curve affects middle values more quickly than values at either the darkest or the lightest ends of the spectrum Gamma contrast values range from 0 0 to 5 0 A value of 1 0 means that no gamma correction curve is in effect the image is displayed at its original levels Gamma contrast changes have similar results to regular contrast changes e Invert reverses all intensities light for dark and dark for light This also will have the effect of complementing colors e g red to turquoise yellow to blue Inverting the image can make certain features easier to see e Pseudocolor applies a false color spectrum to the image This can make it appear in the same colors that a slide might under certain lighting and can be used to highlight specific 44 Doc IT USER MANUAL intensities for analysis e Zoom increases or decreases the apparent size of the image making some details easier to see e Pan Once the image is zoomed in to a larger size it can no longer be shown in its entirety Panning allows you to move the zoom window around the image to display different areas Image Before Effects Were Applied Brightened Inverted Contrast Enhanced To Change Brightness
123. nd displays the Effects tab Select Rectangle Changes the current mouse tool to the Selection Rectangle tool Select Ellipse Changes the current mouse tool to the Selection Ellipse tool Magnify Changes the current mouse tool to the Magnify tool Scale Allows you to indicate a feature and supply its length to set the image s scale Help Shows Help External Application Launches an external application selected in Preferences 16 Doc IT USER MANUAL List of Toolbars The overall toolbar space for Doc It consists of several individual toolbars Each command will appear on the toolbar to which it belongs if it is currently visible The toolbars in Doc lt are e File Contains commands to open and to save files to add profiles to generate reports and tabular reports to export data to change preferences and to print reports e Edit Contains the Undo and Redo commands and the four clipboard commands Cut Copy Paste and Paste Special e View Contains commands that show and hide various main window features such as toolbars and commands that affect how and in what size the current Image window is displayed Also contains commands for 1D Analysis including Area of Interest Lanes Lane ID Lane Names Bands Band ID Lane Curve Lines and RF Lines e Acquire Contains commands to control a scanner and to show the Basic or Advanced Capture tabs of the Capture Panel e Image Contains commands that show the Intensity
124. ned TO A S M Ensure that the batteries were inserted correctly as described in Setting Up the Camera Doc It reports that it can t find the camera Check the camera s USB cable It should be securely plugged into both the output port on the camera and an available USB port on the computer Verify that the camera was set up correctly to receive computer commands as described in Setting Up the Camera Captured images are completely black Check the light source for the hood to ensure it is producing light Snap an image with auto exposure time and auto aperture settings to ensure that these settings are not too low Doc IT USER MANUAL Make sure the camera has power See the Camera seems to have no power troubleshooting section earlier for details Images are very dim or washed out Close the sample loading door on the front of the darkroom hood before imaging Close the sample viewing window before imaging Either set the camera exposure time to a longer time or open the aperture wider by using a lower aperture setting Verify that you are using AN appropriate camera filter for the stain or dye used in the sample Acquire Menu Unavailable Verify that the Security Key is attached to the computer s parallel port See Attaching the Security Key Periodic patterned noise appears in images Check that all cables connecting the camera to the computer are fully plugged in and are not damaged or crimped folded
125. nnccconnnnoconnnnnnnanononnanonononcnnnnonnnnnnnanoss 66 Deleng ARA OLA OM Sr ass 66 To Remove an AMM OA ici 67 CHAPTER ELEVEN VIEWING IMAGE INFORMATION cccoococcocococcononcorocnnnanonnnnnnronnnnnrrnnnnnrrrnannrermananenos 68 V Doc IT USER MANUAL Sls 68 To Display Image Information ccccoonnnnccnccnnononnnncnnncnnonnnonnononcnnnnnnnnnnonnnrnnnnnrnnnnnnrnnronanrnnonanens 69 THEO PIES GCE INOIG S scare T 69 Calibrating mage Scala dd oda used 69 To Calibrate the Image Using the Scale Tool ooccccoconnococcnnnncccononnonanonoconnnnnnnanonnnnanoss 69 To Change Sample Width for an IMage ccocooccccccocnncccocnonoconcnnnonanoncnnonnnononcnnononnnnnnnanoss 70 Mage ISO E 70 TO WIG W IMAGE THISTONY ais rS 71 To Add Notes toa Flstory ENtry i2 0e erorad ed ve Da Rn eia a aite A 71 CHAPTER TWELVE PRINTING REPORTS cooccccccccocccnccoccnnnancnonenannnnrnnnnnnnnnennnannnrrrrnnnnnnrrrrnnnnnrrrrnnanans 72 PRE POMS NA PUE UE 12 TO MIew ang Printa Re DOT tartera odas aaa 73 minm EU REM 14 To RTNcanrimMmades a ein eae a eas 14 CHAPTER THIRTEEN CUSTOMIZING Doc It M 75 GaU T Ue 75 M ltiple Promesa a 75 OPUON SAA A 76 TO Change OPTIONS crm 17 CUSTOMIZING V OOID ANS ii is ai td dia 77 TO CUSTOMIZE TODD it ts 78 Saving S
126. nored in this case e Focus Mode The camera has several focus modes available e Standard Auto Instructs the camera to adjust to and to select the best possible focus on close range subjects automatically e Distance Auto Instructs the camera to focus on objects at larger distances more than 12 which is distant for this application automatically This is the best setting when using a Doc It System e Manual Focus Gives you full control over the focal point for the camera through the Focus Position control a separate control that appears below the Focus Mode Position values less than 120 are considered macro range while those greater than 120 are consider normal range There are also two settings that appear on the Basic and Advanced Capture tabs but that are not actually camera settings e Over Undersaturation Warning If turned on this will apply an over undersaturation pseudocolor to the image after it has been snapped and passed back from the camera The over undersaturation pseudocolor will artificially mark the image bright red where it is oversaturated maximum intensity and medium blue where it is undersaturated minimum intensity also known as zero intensity The pseudocolor does not change or damage the image in any way and can be removed on the Effects tab e Load into Current Image Window If turned on this will reuse the foremost Image window for the next captured image discarding the present image
127. ns through the View menu Doc lt stores the information and makes it your default e View Rulers When you show or hide rulers through the View menu Doc It stores the information and makes it your default By default Doc It always saves implicit changes to your options If you change the default to Ask On Exit you will receive the Save Settings window If you click Yes the changes are saved and the program will appear the next time you open it just as you left it If you click No the changes are not saved and previously saved options or application defaults if you have never saved options apply If you click Cancel the program will remain open for you to exit at a later time You can change the default and remove the message box through the Options tab of the Preferences window 79 Doc IT USER MANUAL CHAPTER FOURTEEN 1D GEL ANALYSIS FEATURES Overview Navigation Finding 1D Gel Lanes and Bands Modifying Lanes Modifying Bands Clearing All Lane and Band Information Related topics OVERVIEW As you use the 1D Gel Analysis tools you will find that Doc It offers several ways to work with the image and to make calculations In this basic section you will learn the following e What features appear on the 1D Gel Menus the 1D Gel toolbar and the Image Window which differ from before e How to find lanes and bands both automatically and manually and how to find bands within existing lanes e How to modify
128. number is provided UVP can create an update file for the additional permissions needed and forward it to a customer site via mail floppy disc e mail or by downloading it over 4 Doc IT USER MANUAL the Internet To Load an Update File When you receive an update file from UVP you can load the new settings by doing the following 1 Open the Key Management screen 2 Select the Open button 3 Select the file from UVP Doc it will verify that the file has not been tampered with It will also check that the file or key currently installed on the system is the correct file or key Make sure the new settings are correct and select the Apply Update button The permissions in the file are moved to the HASP key MOVING FILES FROM THE SMARTMEDIA CARD If you have used the camera to take pictures when it was not attached to the computer Doc It will assist you in moving these pictures off the SmartMedia card in the camera to a directory of your choice All files must be removed from the SmartMedia card before Doc It can proceed with normal acquisition through the camera Doc It uses the SmartMedia card to store images taken during acquisition and needs all the space on it When you start Doc It the application will check the SmartMedia card to see if it is empty If it is not empty you will get a warning message Eom Land ot Empty AX Dig Doc E has Pound existing Files an kte Orme Srta cand LJ Cera so escune
129. numbers click on OK Now the location and dimensions of the band reflect precisely the values you entered Deleting Bands You may choose to delete bands To do so 1 From the 1D Analysis menu select Edit 1D Objects 2 Click on the band you wish to delete A box will appear around the band 3 Onthe 1D Analysis menu select Bands and then Delete Band or by pressing the delete key on your keyboard The band you selected is now deleted You can retrieve the band markings by clicking on Undo CLEARING ALL LANE AND BAND INFORMATION If you wish to begin a new analysis of your image save your existing image with its lane and band information unless you want to start over again Then do a Save As for your new image filing it under a new name and proceed as follows To Clear All Lane and Band Information 1 From the 1D Analysis Menu click on Clear All Lane Band Information 90 Doc IT USER MANUAL All lane and band information will be deleted If you wish to restore information back in to the image click the Undo button on the Edit Menu You may also return to the cleared image by pressing Redo Once you have saved the file however you cannot undo or redo any changes you made 91 Doc IT USER MANUAL CHAPTER FIFTEEN USING THE ID GEL TOOLS FOR MOLECULAR WEIGHT CALCULATIONS Overview Retardation factor Lines Molecular Weight Calibration Applying a Standard to a Lane Removing a Standard from a Lane
130. o see a graph that takes into account the corrected values If you select Rolling Disc a new dialog box appears asking you to enter the desired radius size of the disc DATA EXPLORER AND TABULAR REPORTS Managing Tabular Layouts Doc It allows you to print tabular reports that contain whatever values from the image and analyses you desire The same tabular layouts also are used to view and export data A later section details how to print tabular reports Here you will learn how to create edit delete copy and preview tabular layouts Creating Tabular Layouts x All Data MM Values Concentration Values Edit Delete Copy Preview Cancel 1 Under the File Menu select Tabular Reports You may also select Export from the File menu or under the Data Explorer the Layout button A new window entitled Tabular Layout appears 111 Doc IT USER MANUAL 2 Click on New A second window entitled Create Tabular Format appears Note that it has two tabs Data Points which appears by default first and Alignment 3 In the Name section at the top of the window type in the name of the layout 4 nthe Data Points tab note that all possibilities for inclusion in the report already are selected including Analysis Settings Lane Data Points and Band Data Points De select whatever data sections you do not wish to appear on this report 5 If you wish to include additional band data on the right
131. ocation is outside the Pan rectangle you can simply click the desired location to jump the pan rectangle there Related Topics Chapter 3 Capture Panel Chapter 3 Image Windows Chapter 7 Magnify Tool Chapter 7 Intensity Histogram 48 Doc IT USER MANUAL CHAPTER NINE MANIPULATIONS Overview Revert Duplicating Images Rotate Flip Horizontally or Vertically Despeckle Remove Noise Sharpen Blur Emboss Resize Crop Reduce to Mono Related Topics OVERVIEW Doc It offers ten image manipulations Each manipulation makes a substantial and material change to the image itself In general the results of a manipulation are not reversible Manipulations can be used to correct for problems in preparing for and in acquiring the image They also can be used to expose new information in an image by removing or de emphasizing other information To get the most from manipulations it is important to understand the following features first e Undo Undo reverses the last manipulation performed on an image e Saving Saving stores an image on disk It allows you to return to a former version of an image if you dislike the results of one or more manipulations or would like to try different options e Revert Revert works in conjunction with Save allowing you to return instantly to the last saved copy of an image e Duplicate Image Duplicating an image allows you to try different manipulations on different copies
132. ochrome image For a more detailed explanation see Inside a Pixel PNG Portable Network Graphics a common image format PNG is a lossy compression format that results in very small files Files stored in PNG usually have a PNG extension Pseudocolor Artificial application of color to a non color monochrome image or artificial re tinting of a colored image Doc lt provides several built in pseudocolor sets that mimic certain lighting conditions and reveal specific information in the image Resolution The number of total pixels width of the image in pixels multiplied by height of the image in pixels Higher resolution produces a smoother image especially when zoomed in but requires more RAM and disk space TGA Truevision Targa image format TGA is a lossless compression format that reduces file size somewhat TGA files generally have a TGA extension Thumbnail A reduced size version of an image From thumbnail sketch TIFF Tagged Image File Format a common image format Depending on settings TIFF can be either a lossy or a lossless compression format In Doc It it is used in the lossless mode to reduce image file size without losing integrity TIFF files generally have TIF or TIFF extensions Zoom Factor The percentage by which the image is scaled A zoom factor of 10096 1 0 means that each pixel is not scaled it is its original size Zoom factors greater than 100 indicate that the image has been scaled up meaning that
133. ol whether individual toolbars are shown You can control this by customizing toolbars instead This also is set implicitly when you exit Dock Capture Panel Right By default the Capture Panel is shown on the right side of the Main window when it appears You can make it appear on the left side by clearing this check box Use Toolbar Button Captions By default toolbar buttons do not have text captions You can make them show captions which also makes the buttons larger by selecting this check box e B d 81 IT in Fa dps ees Pura irda Fira Ai a DAMA Moe Ed Sl pe Hard iu HDi mo Changing this check box usually requires some additional effort to arrange the e toolbars appropriately On New Images Prompt for Save Before Allowing Alterations This is set by default and causes the system to prompt you to save a new image before you do anything that might be irreversible If saving the original image is not very important to you you might want to clear this check box so that the message box does not appear Magnify Tool Level By default the Magnify Tool magnifies 3x 30096 above and beyond the current zoom setting This option allows you to increase or reduce the default level of magnification shown by the magnifying glass Recently Used Files List By default the File menu shows the last four image files loaded You can change this number from O to 9 External Application Allows you to select an external program that can be
134. on EllIDSe QO sist a iia 16 Oia e ss PPP c 33 Selection Rectangle tOOl ccccccsccccssccecceeseccceeseecceeseeecseueeeecsugeeecsegeeeesueeeessaseeesseueeessseeeeeessageees 16 ISIN ita no Oca ii 33 SEIECUOM Eee init a Ir 33 A A Sate LI LUE CH 75 107 111 117 Camelia is O o Meditate 24 OPIO Sa ae as a st o ee da a 76 o A 75 e o ete ne ene re eet ner ae ere eee er ee M LM IE ee eee eee ee 79 TOODA Si nee cee eia ae ere eran E Meee i ama 17 MADE y ee AA ec ML EM M ua i ee 55 SNOW Me EE 11 ADOOS esset up tasa ans eu s 61 zelo ee ee 11 Image Actual SIZ C E 18 Mage FO WIN WW ML 18 pigs E ede Gh eee a cele ce ana 18 SAUS AP on ee eer eee 11 nn ee Cen E ee er ee 11 A Se ey E N eee ee 116 Special mci TEE 38 So p ER 20 SHOWING ORIGINO epu tc E 11 A a A N ets tuabac bien S 85 99 104 o net ET 96 SUS tC Intensa a SEES 40 System IRC CUINGIING FILS an A a 1 T Tabular Layout WING Wisteria 113 116 UTI LAY ONS RC DAD MI pM PET 111 S i i ino e EN C E E T CT EUN 111 BIS inre Re EET AT HM TN pM 111 O LE CU MM uiu S MU a ecto pico 111 IN AN ACI Rte NER E TR OD T eC T 111 misure M abana 111 Tapalar WAY OUTS WINGO Wise baii direct tuc im bur ule solita 114 Tapular REDONS ea td pained 106 107 115 A ROMERO 31 123 TECNICA UA e e o ee 9 A TN 26 po crc 31 123 nn A A 123 o A LLLI MEM I LM LS A 31 123 ji THONZO Mallee TET 18 HEC Ca et
135. op down menu under Margins You can make the margins larger or smaller by varying degrees To view the margin lines select Draw Margin Lines 3 To change what appears in the Header Text or Footer Text note the following abbreviations for header and footer text e p puts the page number at the top or bottom of the page c puts the page count at the top or bottom of the page e d puts the date at the top or bottom of the page e tputs the time at the top or bottom of the page 4 Click Refresh Preview near the top left of the window to effect the changes Lane Profile Report To print a graphical representation of the lanes you can select the Lane Profile Fixed Report Doc lt allows you to choose whether to print one or more lanes in the graph To Print the Lane Profile Fixed Report 1 Under the File Menu select Reports and then select Lane Profile A new window entitled Lane Profile Report Options appears 2 In the Lanes section on the left note that all lanes are selected De select whichever lanes if any you do not wish to print out 3 To the right click on the Lane Groupings menu and select how to group the lanes when they are printed Options include grouping all lanes together or printing a certain number of lanes per page If you choose any option except All In One Graph you will be able to select to print the Lane Image as well 4 Select the variables for the x axis and the y axis 9 Select whether to displa
136. ort button brings up a window allowing you to choose where to send the data You also can access this feature using the 1D toolbar Filtering Data Accessible when you create tabular reports or export data the Filter Data button allows you to choose what specific data you would like to appear in reports and in files you export pas Doc IT USER MANUAL Select Data for Allpata O x To Use the Filter Data Button Data 5 Legend qu E pL 1 Under the File Menu select Bred y necu Deselected either Tabular Reports or Analysis Settings Item Selected Export Data In either case S Full Group Selected the Tabular Layouts Window appears Concentration Settings E e Concentration Values EU Lanes Partial Group Selected 0 PV Lane A Select the name of the report 212 Lane B or file you would like to work cw Lane C with oo Lane D 212 Lane E 212 Lane F Lane G Sei Bands Click Preview or Export depending on whether you are creating a tabular report or exporting data A new E 2 Bands From Lane window appears El Bands From Lane B In the new window labeled E Bands From Lane C Select Data for the file Ed Bands From Lane D notice that there are three EJ Bands From Lane E main groups Analysis Ed Bands From Lane F Settings Lanes and Bands El Bands From Lane G To remove an entire group e g all band information de select the button next to Cancel that g
137. os 4 To Load an Update Ele o mun a eue ied re 5 Moving Files from the SmartMedia Card ooccconcccccncoccccccncocnconnnconnnnocnnnnnnonnncnnnnnnnnnos 5 To Move SmartMedia Card Files to a Hard Drive Location ooccccocccccocncccnnnnccnnnnnonononaninnns 6 To Delete SmartMedia Card FilesS ooccconccconncocnncocnncocnnonnnononocornnonnnnonnnononnnnnnnonnnonrncnnnanonos 6 CHAPTER TWO TROUBLESHOOTING 25 2 52 ects tatedsccathiwans bateessvandt esta hated ue ao sce eran devi EE A A DECRE 7 UsSNg ONNE Nel anni iii 7 SNOWING us jo 7 A ne ee eee T PICT O ONIN CAMO cR EE a eee oe ccm DP 7 Troubleshooting Mie H 8 Technical SUP DO aid 9 Camera Technical UP lee lata 9 Doct Te CHIC AN SUN O A NEES 9 CHAPTER THREE NAVIGATION aa aa AA AEA 11 Main WINGOW sist id Kant idle Do a Od 11 To Show or Hide the Toolbar ccoocccocnccoocnconcncoonnnocnnonnncnonconrnnoncnnnnnncnnnnonnnnonnconrnnnnnnnnnnnnns 11 To Show or Hide the Status Bar occccoccccocnccccnconnncocnonononorononcnnonrnnonnnononnonrnonrnnonnnnonnnnnnnnnns 12 To Show or Hide the Capture Panel x roo a desi e eei ne Ro Gottlob i Roe Were 12 E INE A Er ase seanaaea seaman eeaesenaet oc aedecnnad parecaneascenencense 12 TOMAS a A UM E ande ide Dr c 16 Iria Toolbar BUUONS eiie dieu e chat ER ee Uo Opto NE SE p
138. ove e When the change occurred e What the change was and details about it e Any notes that you add to explain the entry 702 Doc IT USER MANUAL aj Image Le pre ation Xj Tope Commen Dee TRA 1251 PM To View Image History 1 Ifthe image is not the foremost image select it from the Windows menu or click its title bar 2 From the View menu choose Image Information The Image Information window will be displayed 3 Click the Image History tab at the top of the window 4 Click on any history entry in the list on the left side to display details about the entry To Add Notes to a History Entry 9 Click OK Related Topics Chapter 6 Paste Special Chapter 7 Rulers Chapter 8 Effects Tab Chapter 9 Manipulations Chapter 10 Types of Annotation 274 Doc IT USER MANUAL CHAPTER TWELVE PRINTING REPORTS Reports Image Properties Notes History Image and Properties Image and Notes Image and History O e O O O O O Image Properties Notes and History Print Command Related topics REPORTS Doc lt provides eight reports Image Report Prints the image using as much of the page as possible while preserving the image s aspect ratio Properties Report Prints the image s resolution width and height depth scale and file information Effect Settings Report Prints the setting values from the Effects tab Notes Report Prints the image notes as ent
139. ow of the report appears 2 Select Print To Change General Layout Before Printing 1 To change the title of the report as it appears on the printout type the new name at the top 2 To change the margin size click on the drop down menu under Margins You can make the margins larger or smaller by varying degrees To view the margin lines select Draw Margin Lines 3 To change what appears in the Header Text or Footer Text note the following abbreviations for header and footer text 8 Click Refresh Preview near the top left of the window to effect the changes pi You also can access this feature using the 1D toolbar Analysis Bands Doc It prints reports detailing band analysis The Analysis Bands Fixed Report offers the following information e The Band Name and ID e The calculated peak values Rf value and molecular weight e The intensity of the band including its maximum volume percentage of the lane and mass and e The concentration of the band including its maximum volume percentage of the lane and mass 119 Doc IT USER MANUAL To Print the Analysis Bands Fixed Report 1 Under the File Menu select Reports and then select Analysis Bands A preview window of the report appears 2 Select Print To Change General Layout Before Printing 1 To change the title of the report as it appears on the printout type the new name at the top 2 To change the margin size click on the dr
140. p puts the page number at the top or bottom of the page 5 c puts the page count at the top or bottom of the page 6 d puts the date at the top or bottom of the page and 7 t puts the time at the top or bottom of the page 8 Click Refresh Preview near the top left of the window to effect the changes EXPORT DATA Doc It allows you to export data to Microsoft Excel or to other software packages for further analysis To do Under the File Menu select Export Data The FF Data Esport DAA Mancha Tabular Layout window appears Export Select the report you wish to export Click Comma Separated Export C Tab Separated C Space Separated CC Other A new window appears asking you to select what data you wish to be exported Select or de select whatever parts you wish to see To Excel exported or not T i Click OK A new window appears entitled Esports Data Export Select whether you wish to export the data by Comma Tab Space Other where you type in the delimiting character or characters or To Excel Click Export Data If you select To Excel the Excel program will open up with the data in it If you select one of the other options you will be asked to select the file s destination Enter the destination and click Save mo You can also export from the Data Explorer oO 116 Doc IT USER MANUAL FIXED REPORTS 1D Fixed Reports Doc It offers four reports that you cannot alter b
141. ph From the menu you can display a lane profile graph e View Analysis Objects Selecting this feature displays all analysis objects while de selecting leaves the original image untouched e Find Lanes and Bands From the menu finds lanes and bands 1D Gel Preferences The User Preferences window has an additional tab that allows you to set preferences specific to the 1D Gel Analysis system This tab has two sections Toolbar settings and Defaults Pisererces Vibe Cpl boa Anal Toobar i Top C Bottom Let 7 Rigi Ee Vus TD rahas Took o Lise bool button capice ies Hues of iea BS iai Lanas 9 yis Lane ID e Lara ama D Via Lara Curves Lines iaa AP Lines h View Bands E Ve Bard ID Lame vadih 6 constant across al lares hi Force al lares otraighl he The lane volume i de sum of al de bend Factory Setting Choe You can set up the 1D Gel toolbar using the following controls e Align Analysis Toolbar Select the position of the analysis toolbar It can be docked to the top bottom left or right of the Image Window e View Analysis Toolbar Allows you to turn the analysis toolbar off providing more screen area for images e Use Toolbar Button Captions Turns toolbar button captions on or off Toolbar button 84 Doc IT USER MANUAL captions identify each toolbar button making them easier to use but uses more screen space for the toolbar Toolbar settings are remembered in your
142. profile and reset the next time it is loaded They are not saved with specific images You can also set the following defaults e View All the various view defaults allow you to determine whether by default the analysis feature named should be shown e Lane Width is Constant Across Lanes Forces all lanes to be the same width e Force Lanes Straight Creates only straight lanes no automatic curving You can override this by manually or automatically curving lanes during the Find Lanes and Bands operation or on an individual basis using the Auto Curve Lanes menu option e Lane Volume is the Sum of Bands Lane volume for concentration purposes can be calculated either using all pixels in the lane s area or using only those pixels that fall inside bands in the lane Setting this value off means that all pixels in the lane will add to the lane s volume and the sum of all band volumes will usually be somewhat less than the lane volume Setting this value on means that the sum of all band volumes will add exactly to the lane volume and band percentage of composition values will generally be higher than if the value is off Defaults only apply the first time you start an analysis after that Doc It remembers the last setting you used on that analysis and restores it 1D Gel Analysis Settings 1 To access analysis settings go to the View menu and then select 1D Analysis A new window appears entitled Image Information m mage In
143. r the application toolbars user preferences and camera capture templates if they have capture permissions according to how you saved the settings during the last time Doc It closed while in that profile This selection allows you to customize the windows and toolbars you see At any time you can change the selected profile the system will restart to effect the changes One default profile called Public cannot be removed It is the default profile for the system If you prefer to only use the Public profile you can de select the Preferences dialog window under the File menu The next time you start Doc It you will not be prompted to select a profile Instead the Public profile automatically loads z 75 Doc IT USER MANUAL OPTIONS You may set a number of options in Doc It to customize the look and the feel of the application They are View Capture Panel Controls whether the Capture Panel is shown or hidden by default This also is set implicitly when you exit View Image Rulers Controls whether image rulers are shown or hidden by default This also is set implicitly when you exit View Annotations Controls whether annotations are shown or hidden by default This also is set implicitly when you exit View Status Bar Controls whether the status bar is shown or hidden by default This also is set implicitly when you exit View Toolbars Controls whether all of the toolbars are shown or hidden by default It does not contr
144. rger depth of field A large value indicates a narrow aperture which restricts light and results in a darker image and a narrower depth of field If the Aperture is set to Auto the camera will adjust it to match the exposure time unless this is also Auto and the current lighting conditions e Compensation A fudge factor that affects how the various automatic modes work A negative value results in a darker image a positive value results in a lighter image Zero 0 is the default automatic behavior e White Balance Affects how the camera deals with white intensities adjusting for various kinds of off white conditions Conditions for which the camera can adjust include auto camera selected daylight no adjustment fluorescent artificial lighting tungsten artificial lighting and overcast cloudy daylight e Light Source Adjusts compensation and white balance see above on the Basic tab according to the light source UV or white light in use e Light Metering Determines how the brightness levels for the camera are set Normal mode sets levels from the entire image Spot metering sets the levels from the center of the image only and is used mainly to separate a central foreground from background Either Normal or Spot can also be used in Macro mode which will be the appropriate setting for the camera while in the hood e Flash Mode Determines whether the flash will be on or off and whether it will use red eye reduction by
145. roup To remove only specific items of information about Lanes or Bands or Analysis Settings de select the box next to those particular items The legend area next to the data selection area indicates how to tell whether you have nothing selected a whole item selected a full group selected or a partial group selected TABULAR REPORTS In Tabular Reports you can print whatever data you select about the image and the analyses you have performed on the bands and lanes To Print Tabular Reports 1 Select Tabular Reports from the File Menu A new window pops up 2 Select the name of the report you wish to print from the list Click Preview 3 Anew window appears asking you to select data for the report Filter data by selecting or de selecting whatever you would like to include in the report 4 Click OK A new window appears with a preview pane of the report 5 Click Print ro You can also choose to print from the Data Explorer 115 Doc IT USER MANUAL To Change General Layout Before Printing 1 To change the title of the report as it appears on the printout type the new name at the top 2 To change the margin size click on the drop down menu under Margins You can make the margins larger or smaller by varying degrees To view the margin lines select Draw Margin Lines 3 Tochange what appears in the Header Text or Footer Text note the following abbreviations for header and footer text 4
146. rt 1 Ifthe image is not the foremost image select it from the Windows menu or click on its title bar 2 From the File menu choose Reports and then choose the report you desire 3 To change the target printer paper paper source tray or page layout click Page Setup and make the desired changes 4 To change the header or footer text type new text in the text box and click Refresh Preview There are some special character combinations you can use in the header and footer Zp is replaced with the current page number d is replaced with the current date Zot is replaced with the current time 9 To change the margin choose an alternate margin setting from the Margins drop down list 6 Select Draw Margin Lines to see the margins graphically When the preview looks correct click Print M Cm Doc IT USER MANUAL PRINT With Doc It you can print your images to any Windows supported printer crm The Print command uses exactly the same format as the Image Report in Reports O To Print an Image 1 If the image is not the foremost image either choose it from the Windows menu or click its title bar pi The Print command is also available on the Files toolbar but does not show the Page Setup dialog window Instead it prints an Image Report directly to the default printer 2 From the File menu choose Print 3 If necessary choose the target printer paper size paper source tray and p
147. s Pile Hare LUPE de py Fis Pat CE nana Peete NEP Salar Pack agen T robur Developmen H sp Printed Mosa af Lead BAA 1 41 55 PH ue T KE 74 145 Eher 68 Doc IT USER MANUAL To Display Image Information 1 Ifthe image is not the foremost image select it from the Windows menu or click its title bar 2 From the View menu choose Image Information The Image Information window will appear 3 To switch between Image History and Properties click the appropriate tab at the top of the window gt Image Information is also available on the toolbar and through a shortcut menu on the image itself To Enter Notes Display the Image Information window as described above 1 i i 2 In the Properties tab type your information into the Notes text box 3 Click OK CALIBRATING IMAGE SCALE Each image in Doc It has a scale associated with it Scaling information is used to display rulers length measure and area measure annotations Doc lt automatically calibrates images taken with the camera and darkroom Images taken with the camera outside the hood will be calibrated incorrectly Images scanned into the system from a scanner or imported from another program are not calibrated at all In these two cases therefore you may wish to adjust or to set the image s scale An uncalibrated image will have Pixels as the unit type If the unit type is Pixels the number of units is the number of pixels in the i
148. s Settings and e In Lane Properties This section covers Lane Properties To View and Use Lane Properties From the 1D Analysis Menu select Lanes and then select Lane Properties A new window 106 Doc IT USER MANUAL appears In this window Doc It allows you to perform various changes to the lane ON a C nios ma xj You can name the lane Lane ID C Mare You can alter the color of the lane Lana Color You can change the geometric Cunent Color LF Greer MI proportions of the lane or of all of the lanes if you have selected to make all Geometry Lares lanes the same width and TE dia fess dm jai 47 TA PIE mn ee You can change the molecular weight Molecular Weight Standard Standard of the lane if you have Change performed a molecular weight calculation Values Mas Ling Hame You can change the mass assigned to no rm the lane Inerisdu Plasme Irteristy Volume X9 es Lane Properties also offers you the following Goncertraticar Macau Corcaritratica ohne information HJA HJA The Lane ID The unit of mass Cancel l l The intensity maximum The intensity volume The concentration maximum and The concentration volume m You may also access this feature by right clicking on the lane and selecting Lane Information in the shortcut menu or by using the 1D Toolbar BAND INFORMATION In Doc It you have several ways of viewing band information e In the
149. s ili nor be operable undi Files ae i r rareidl ros Lra card i demie dpe r che ire dable After you click OK Doc It will show you the pictures or movies currently on the SmartMedia card and ask you what to do with them Camera tik Files Fourad Pio oon JPG PUT TEE LEE RET Doc IT USER MANUAL At this time either you can transfer individual files or all files to a location on the computer hard drive or you can delete any or all files To Move SmartMedia Card Files to a Hard Drive Location 1 Select an individual file or click Select All to select all files 2 Click Transfer to transfer the files A dialog window will appear 3 If you selected an individual file select both the file name and directory location in the dialog window Click Save to transfer the files OR If you selected all files select the directory location Transferred files will retain the file names they have on the SmartMedia card Click OK to transfer the files To Delete SmartMedia Card Files 1 Select an individual file or click Select All to select all files 2 Click Delete to remove the files from the SmartMedia card A warning box will appear 3 Click Yes to remove the files Files removed in this manner cannot be recovered Related Topic Chapter 2 Troubleshooting Doc It Doc IT USER MANUAL CHAPTER TWO TROUBLESHOOTING Using Online Help Troubleshooting Tips Technical Support Related Topics USING ONLIN
150. severable from this License and shall not affect the validity and enforceability of any remaining provision This is the entire agreement between the parties relating to the subject matter herein and shall not be modified except in writing signed by both parties Doc IT USER MANUAL CHAPTER ONE WELCOME To Doc IT Overview of Application Features System Requirements Installation Instructions How to Start the Application Moving Files from the SmartMedia Card Related Topics OVERVIEW OF APPLICATION FEATURES Doc lt is an imaging and analysis application that allows you to capture manipulate and analyze images simply and efficiently You can use Doc lt to image electrophoresis gels using a digital camera with the quality you would expect from a much larger system Once you have captured an image you can save it for your records use various effects to show hidden detail manipulate it to set it up for better analysis annotate it to point out key features and perform 1D analysis SYSTEM REQUIREMENTS NOTE When using the camera for bioimaging capture the CAMERA The minimum system requirements for Doc lt are d 1 CONTROL setting must be ON e Internet Explorer 6 or higher e Windows 2000 or XP Professional e Intel Pentium lll or 4 processor 800mHz or higher processor clock speed e 256 MB RAM 512 MB RAM recommended e 100 MB of available hard disk space e 32 MB of VRAM Video RAM or greater e CD ROM drive e
151. side of the window select Include Band Totals and or Grouped with Lane Selecting Band Totals means a new row appears below each group of bands giving totals for the columns Choosing Grouped with Lane means that lane data will be included with the band data 6 Click OK The first window appears with the new layout listed Editing Tabular Layouts 1 Under the File Menu select Tabular Reports A new window entitled Tabular Layout appears 2 Select the report listed that you wish to edit Click on Edit A second window entitled Edit Tabular Format appears 3 In the Data Points tab select or de select whatever data sections you do or do not wish to appear on this report 4 Click on the Column Order tab of the window 5 If you wish to change the order of any section in the printout report highlight the section and then click on the up or down buttons to the right 6 To change the name of the column the alignment of the column caption or the alignment of the data click Edit in the upper right corner of the window A new window appears 7 n the new window type in a different name for the column Here you can also change the alignment of both the data and the caption from left to right or center 8 Click OK The changes are now in place 9 To preview the report click Preview A new window appears that summarizes the data that will be included in the report Click OK 10 Another window appears entitled Analysis Tabu
152. ssed in the next chapter An image acquired in any of these fashions will appear in its own Image window A Doc IT USER MANUAL OLYMPUS CAMERA Basic Capture Tab m E The Basic Capture tab is one of three tabs that make up the Capture Panel Msn 1 9 It provides simple camera controls that produce good images under most Hr conditions It also provides an easy to understand and quick way to image aa slides or Up ar a nin T esiri lr coupe oar The Basic Capture tab offers the following settings and controls e Exposure Time Controls how fast the shutter is snapped e Resolution Controls the number of pixels captured More pixels high resolution produce a higher quality image but also take considerably more disk space e Light Source Adjusts automatic exposure for the type of light source in use e Sample Size Controls the zoom setting and thus how large or how small a sample appears within the image bounds let pa ee an e Color Capture Determines whether the camera captures an image in color or monochrome e Over Undersaturation Warning Controls whether a special pseudocolor is applied to the resulting image which indicates oversaturated and undersaturated areas with red and blue respectively e Load into Current Image Window Controls whether the new image should overwrite the foremost existing one or create a new Image window It is more efficient to keep just the latest image however this would not
153. stretched or squashed Bits The smallest units of computer measurement A bit is a single binary value i e it can be on or off only Bits typically are combined into units of eight called bytes Modern computer processors work with groups of 4 32 bit processor or 8 64 bit processor bytes at a time BMP Microsoft Bitmap image file format BMP is a lossless format which provides some compression to reduce file size BMP files generally have a BMP extension Control Handle A small square at the corner or similar point of a graphical object that marks its extent and indicates that the object is selected Usually the object can be resized by dragging the control handle in some cases different behavior results Electrophoresis The movement of suspended particles through a fluid or gel through the application of electrical current to the suspension medium Fidelity The degree to which an image is true i e accurate and uncorrupted to the original scene it represents Also used in audio technology with the same meaning GIF Graphic Interchange Format a proprietary Xerox image compression format GIF is a lossy compression format that results in very small files Files stored in GIF usually have a GIF extension Image Depth The size and thus range of intensity numbers supported per pixel in an image Doc It supports two depths 8 bit in which intensity numbers range from 0 to 255 and 16 bit in which intensity num
154. t 5 before the first manipulation you select 2 On the Rotate window type the desired number of degrees into the Angle text box 3 To rotate the image clockwise by this number of degrees select Align To rotate counter clockwise by this number of degrees select Rotate 4 Click OK Rotating a large image can take fifteen seconds or more from the time you click OK Rotations by 90 180 or 270 degrees do not degrade the image These operations can be completely reversed by a rotation of the same amount in the opposite direction 53 Doc IT USER MANUAL FLIP HORIZONTALLY This manipulation mirror images an image right for left Unlike most manipulations it does not degrade the image and may be used repeatedly with no ill effect Two uses of the manipulation will return the image to its starting orientation To Flip an Image Horizontally 1 If the image is not the foremost image select it from the Windows menu or click its title bar 2 From the Image menu choose Manipulation and then Flip Horizontally cun If the image has not yet been saved you will be prompted one time to save it before the first manipulation you select FLIP VERTICALLY This manipulation mirror images an image top for bottom Unlike most manipulations it does not degrade the image and may be used repeatedly with no ill effect Two uses of the manipulation will return the image to its starting orientation To Flip an Image Vertically
155. t portion of the Help window Help Conventions The note icon indicates an important point that you will need to be aware of to use Doc It properly Doc IT USER MANUAL p The tip icon indicates a trick or technique that may help you work more efficiently The techniques described in tips are never required to run Doc It just useful A The Under the Microscope icon indicates a detailed technical or scientific We reference topic You won t need to understand these topics to use Doc lt e E Si the Micro Text that is blue and underlined in Online Help is a link to another topic In most cases you will find these links at the bottom of the help window under Related Topics Text that is green and underlined in Online Help is a link for a word definition in that case the word will appear in a pop up window with a pale yellow background TROUBLESHOOTING TIPS Doc It Software displays an error message Doc lt requires Internet Explorer 6 0 or upon initial start up higher to be installed on the computer Install Internet Explorer 6 0 which is located on the Doc It CD in the folder titled Internet Explorer Versions IE6 setup folder IE6setup exe Camera seems to have no power Check the camera s power adapter It should be securely plugged into both the wall or the surge protector receptacle and the camera s input power receptacle Make sure the camera is turned on The dial on top of the camera should be tur
156. tch the bands you may choose to use the stretch factor 1 Ensure that Manual Mode is de selected 2 Drag a known weight up or down with the mouse until it matches the appropriate band Alternatively you can select the weight with the mouse or TAB key and move the weight up and down with the UP and DOWN arrows on the keyboard this helps adjust the weight by small amounts When you have a match of the weight with the band the line color changes from blue to yellow default colors 3 Adjust the stretch factor scaling between weights until the other weights match their appropriate bands You can adjust it using the mouse wheel rolling up increases the value rolling down decreases it or you can enter a new value into the text box and click Set 4 Click OK to save the calibration crm Using the Stretch Factor gives you a weight match on the band up to 5 of the 5 weight you assigned To obtain exact placement on the band use the manual mode described below Using Manual Placement of Weights If you do not want to use the Stretch Factor you can also adjust weights individually using manual mode 1 Select Manual Mode 2 Move each weight separately with either the mouse or the keyboard arrows to position them exactly on the band Weights cannot pass one another so it is usually best to start with either the lightest or heaviest weight and work toward the other end Exact Placement of Bands In Manual Mode
157. te Ena Did Dia dh 2 Height e QUK Cercs To Resize an Image 1 If the image is not the foremost image select it from the Windows menu or click its title bar 2 From the Image menu choose Manipulation and then Resize The Resize window will appear If the image has not yet been saved you will be prompted one time to save it before the first manipulation you select Select the desired new size from the drop down list of suggested sizes OR Select the Enter Desired Dimensions option and type either the desired new width or the desired new height cun If you wish to distort the image you can clear the Constrain Proportions check box and type the new width and height This should be used only to reverse a similar distortion created in the image capture process 4 Click OK Resizing a large image may take a few seconds CROP This manipulation removes unwanted edges reducing the image to a more concise region of interest To Crop an Image 1 If the image is not the foremost image select it from the Windows menu or click its title bar 2 Using one of the selection tools select the region you wish to keep 3 From the Image menu choose Manipulation and then Crop If Crop is unavailable the most likely reason is that there is no selected area marked cun If the image has not yet been saved you will be prompted one time to save it E before the first manipulation you select
158. te Molecular Weight cocoooccocococnococononccconnonoconnnnnonanoncononnnnononnnnnnnnnnonannnnenonnnnnnnnanass 82 A A To tales a S yarecceesnuuesecs see hes cence dabas ose urne 21 Aavanced Capt e ace areas orcas 23 A TED Tr 24 BASIC CAD m arses 22 Capture Templates untitled iu ttt bestiae desti dit iii 26 O m E 24 E A NEAS 18 o iis tokens essi Moos de dott ahs alae LM oou aloes atcur da des Mot cL A a ahaa le ase 23 A 22 Templates xum 26 A o et ree ee 26 E e meee i eee ee en Ome Eu EM E ME 26 Del PC 26 A ae eee uL MI E IL hund uui Eu 26 A uec eue uc d E EE Ei E uui I Ms 23 Caprin dde S chu tm MED a qM ee 22 Change Axis Variable S 5 a feci vedette iue 109 Change General Layout Before Printing cococccncocccnnoconcnnccnnnnncnnancnnonononnnnos 115 117 119 120 AA M 56 SITIS dl rca 82 90 eo e 116 COMES A do 23 LESS Sr ds 122 LOS Vpn 122 epe RERUM E 106 109 Contents iia a 7 125 Doc IT USER MANUAL Context Menu Command usina e odds 83 CODY MD 34 PIliptiGale Sha Desi api 33 ENS Mage ninio 34 Rectangular Shapes 000 ia iia 33 o A A 51 Copying Tabular Hay Outs stas is o a Ol ces 111 Corrected Made iii a A AA O 99 101 Corrected Male Ss cono O O iaa 99 110 120 Creating Anota HONS ts a a A 62 A E ALAIN ch ata MM LOU t nated M Rer I nese ale 58 CUNE MOGI use oct utut metet u
159. ter 8 Effects Tab Chapter 8 Zooming and Panning Chapter 10 Length Measure Annotations Chapter 10 Area Measure Annotations Chapter 11 Image Information Chapter 11 Calibrating Image Scale 43 Doc IT USER MANUAL CHAPTER ElGHT EFFECTS Effects Brightness Contrast Gamma Invert Pseudocolor Zooming and Panning Related Topics EFFECTS TAB iia This tab of the Capture Panel offers features to control how an image m FT ll looks None of the Effects makes permanent changes to the image A You can reverse most of the Effects everything except the zoom ime o setting with the Reset button Ded mage Er o The specific features available on the Effects tab are e Brightness affects the overall brightness or dimness of the image A brightness level of 50 means that the image is displayed in its original brightness i e unchanged Changing the brightness level can make features near the top or the al bottom of the intensity scale easier to see e Contrast affects the difference between light and dark parts of the image A contrast level of 50 means that the image is displayed in its original contrast A level higher than 50 means that contrast has been increased lights are lighter darks are i darker A level lower than 50 means that contrast has been I es decreased lights and darks are both closer to middle values Increasing the contrast tends to highlight differences i
160. the line thickness must be 1 and the Line Thickness menu will be unavailable The same annotation types that support Line Style support Line Thickness e Arrow Style You can choose whether a Line annotation only has o No arrowheads o An arrow at the start first point of the line o An arrow at the end second point of the line o Arrows at both ends of the line e Font Size You can choose the font size of Text Length Measure Angle Measure and Area Measure annotations from among the listed values e Bold You can choose whether Text Length Measure Angle Measure and Area Measure annotations should be boldfaced e Italic You can choose whether Text Length Measure Angle Measure and Area Measure annotations should be italicized e Underline You can choose whether Text Length Measure Angle Measure and Area Measure annotations should be underlined To Change the Format of an Annotation 1 Select the annotation by choosing Edit Annotations from the Tools menu then click on any part of the annotation 2 Change the formatting options using the Formatting menu You can customize the Formatting toolbar to show drop down buttons for formatting options There is also a shortcut menu for annotations that offers the same formatting choices as the Formatting menu DELETING ANNOTATIONS Deleting an annotation removes it permanently from the image 66 Doc IT USER MANUAL To Remove an Annotation 1 Select the
161. tightly back on themselves Ensure that devices that may generate electromagnetic interference such as fluorescent lighting is not overly close to the camera cabling or computer TECHNICAL SUPPORT Camera Technical Support If you need help or support for the camera itself please refer to the product information provided with your camera Doc It Technical Support If you need support for the Doc It software you can contact UVP via e World Wide Web http www uvp com e 909 946 3197 or toll free technical support line 800 452 6788 e Email techsupport uvp com e Fax 909 946 3597 e In Europe call 44 0 1223 420022 or fax 44 0 1223 420561 e Email uvp uvp co uk Please have the following information ready when contacting UVP e The version number of your Doc It software To find your version number choose About from the Help menu The version number will appear in the About window e The type of computer you are using including processor type operating system and RAM if you know these To find this information choose About from the Help menu and click System Info A summary of your system information will be displayed 9 Doc IT USER MANUAL e A description of the problem you are having including what you were doing when the problem appeared Please make note of exact wording of any error messages 10 Doc IT USER MANUAL CHAPTER THREE NAVIGATION Main Window Menus Toolbars Capture Panel
162. to an image in order to make it store more compactly on disk Typically formats that use lossy compression store in much less space than lossless compression formats By comparision a lossless format does not store as compactly but also does not change the image in any way The Extended Attributes File The image will also have a second file that ends with the extension EXT This file contains the image s effect settings history scale and annotations It will appear in the same folder as the image file and will have the same name with the image s extension added to the end For example if the Image File is named Mylmage JPG the matching extension file would be MylmageJPG EXT If you wish to copy an image move an image or send an image to another Doc It user you should copy move or send both files Related Topics Chapter 4 Acquiring Images 234 Doc IT USER MANUAL CHAPTER SIX EDITING Overview Undo and Redo Using Selection Tools Copy Paste Paste Special Related Topics OVERVIEW The image editing features provided in Doc It allow you to undo changes to images to copy images or parts of images to paste images from the clipboard as new images and to merge clipboard images with existing images using the Paste Special feature Most editing features are found on the Edit menu However to be able to use all editing features you will also need to use the Selection Rectangle and Selection Ellipse tools from the
163. tored and how to move image files around on disk or to send them to another Doc lt user see Image Files es T q A P rr dms iM To Load an Image 1 From the File menu choose Open pi You can also use the Open button on the Toolbar 2 Select the type of file you wish to open If you re not sure of the file type select Image Files If the file has an unusual extension you may want to select All Files instead 3 Navigate through your disk drives to the file folder in which the image is stored Doc It keeps a folder structure of its own that it will show by default Most images will probably be in this folder 4 Select the desired image file 5 Click Open An Image window containing the desired image will appear To Load a Demo Image 1 From the File menu choose Demo Images 2 Select the desired demo image file from the list of available files 3 Click Open An Image window containing the desired image will appear 29 Doc IT USER MANUAL SAVING IMAGES You can save images acquired in Doc It so that you can continue to work with them in later sessions keep them as records or load them in other software packages Images can be saved to any disk drive media including floppy disk Zip disk removable hard disks and hard disks A NE 33 EG mrerm Da gr Mathie pa MEE M Acquire p M rr pg I Lm od Eel ap pm W I ecstatic I Lm cd rr E IN soe oci Cope pa
164. trophoresis gel You can select the color line thickness line style solid dotted or dashed font size and formatting bold italic or underline of an Angle Measure annotation e Area Measure Area Measure annotations look somewhat like Rectangle annotations except that they show the area of the rectangle in image scale units see Rulers You can select the color line thickness line style solid dotted or dashed font size and formatting bold italic or underline of an Area Measure annotation ro Length Measure and Area Measure annotations use the image s scale in calculations If these annotations display information in pixels px no scale has been set See Changing Sample Width for instructions on setting the image s scale CREATING ANNOTATIONS You can create annotations using one of eight annotation creation tools one for each type of annotation The tools which appear on the Tools menu are Text Line Rectangle Ellipse Highlighter Length Measure Angle Measure and Area Measure All instructions below assume the desired image is foremost If it is not select it from the Windows menu or click Its title bar To Create a Text Annotation 1 From the Tools menu choose Text 2 If desired select the color font size and formatting bold italic underline from the Formatting menu 262 Doc IT USER MANUAL 3 Click the position on the image where you would like the text annotation to be The Text
165. ups EE omia aaepe e di Le do 16 EISUOL TODD Sart dado acia 17 FRO AITANGING VOONDANS 3 m m TM 17 Capture RMN els it as 18 Mage b Aislo o Te 18 Doc IT USER MANUAL Organizing Image Windows c cooocccccoccnnoconcnnccnononcnnnonnonononononcnnnnnnnnnnnnnnrnnnnnnrnnnnnnrnnnnanennnnanens 19 Information Provided by the Image Window cccccocccnccnoccnconccnnoconcnncnnnccnconononnononcnnnnncnnnonanennos 19 Stats Da Em 20 CHAPTER FOUR ACQUIRING AND MANAGING IMAGES oooocccccoococcccncnoancnnnenanancnnnnnananronnnananenennnanans 21 A o y O 21 OlVIMDUS CAMERA rr diodes 22 Basic Gap Tabrac it T UE 22 Advanced Capture Tab e tao 23 Camera SeN Suidam an a cin 24 Capture Temas a a a a a 26 SCANNING IMAGES asse e E 2f To Select the Desired Scanner aii A A 2f To Scan an Image from a Scanner cccccceececceesececeeeseecceeucecceegececeuseeessageeecseuseesssaseesssaees 27 CHAPTER FIVE LOADING AND SAVING IMAGES ooooncccccoococcccccnnonnccnnenonancnnnnnannnronnnannnerrnnnannnerrnnaannss 29 ESAadIna IMageS ica til ia cel e TL LE 29 TOs OG an MIS did tape 29 To Load a Demo Maderas 29 Saving IMA ri a ao 30 tTO Savea New Image simile solo ld iio enl uer tuu pd hod DU TUE 30 To Save Changes to an Image sese nennen nnne nnns 30 To Save Using a Different File Folder Name or Type oooccccccocccccccnccnonoconcononcnncnnnnnnconancnonanons 30 A ley tie Dredge deitaa bote ecLee ise Lqrd aS RET
166. ut that provide you valuable reference information e The Analysis Settings Report Gives you information on Background Color and Correction lane width and volume and whether the lanes are straight e The Analysis Lanes Report Gives you information on Lane ID and name band count in each lane concentration intensity and mass e The Analysis Bands Report Gives you information on Band ID and name calculated peak values intensity and concentration and e The Lane Profile Report A graphical representation of lane data Analysis Settings One fixed report that Doc It offers is the Analysis Settings Report This report gives you information on the following 1D Gel Analysis Settings e Background Color e Background Correction e Disc Radius If you used Rolling Disc e Whether Lane Width is Constant Across All Lanes e Whether all lanes were forced straight and e Whether the lane volume is the sum of all of its bands To Print the Analysis Settings Fixed Report 1 Under the File Menu select Reports and then select Analysis Settings A preview window of the report appears 2 Select Print 117 Doc IT USER MANUAL F F 3 1d E zu E i m za E zem ox ur mi m Pp E YES So SB Se 585 pia E ws Hs Sy EE Gees i TEHETI ag EH Ns Xa i n i E INEA m a os ir HAGA RS puro dpo d o Wt Cue F hus RO Um FETAL En AE U Cher E AE EPT pus E Ju Ff FF FF OQ UE ts mos Bel ee ee es Pee um
167. value of the standard After entering the numerical value click on Add again for as many values as you wish to enter Click OK on the right side The first window appears again with the new standard entered Editing a Molecular Weight Standard to the Library 1 Select the Lane to calibrate and click on it 2 Underthe ID Analysis Menu select Lanes and then select Calibrate Molecular Weight A new window appears 3 In the new window select the standard you wish to edit Then click on Edit 4 Now you can change any of the information in this window including group name units or most commonly weight 5 Click Edit to reflect the new change and then click OK Deleting a Molecular Weight Standard to the Library 1 Select the Lane to calibrate and click on it 2 Under the ID Analysis Menu select Lanes and then select Calibrate Molecular Weight A new window appears 3 Inthe new window select the standard you wish to delete Then click on Delete Doc It asks you in a pop up window if you want to delete that standard Select Yes if it is correct No if it is not 95 Doc IT USER MANUAL 4 Click on Cancel to return to the image window Copying a Molecular Weight Standard in the Library 1 Select the Lane to calibrate and click on it 2 Under the ID Analysis Menu select Lanes and then select Calibrate Molecular Weight A new window appears 3 In the new window select the standard you wish to copy
168. ve Lines vertical lines down the center of each lane that allow you kaza biad p to control lane curving a prs ELE z L1 Jeep ve Bands marked by horizontal lines at i hen a the band peak Rf Lines white lines interrupted by erp small white circles at each intersection of the Rf line and a lane In addition to the objects above there are also some 1D gel text labels that help you identify data in the image The labels cannot be directly manipulated These labels are e Lane IDs Letter codes at the top of each lane Calibrated lanes are indicated by showing the lane ID in brackets e g A as opposed to A e Lane Names Names you entered in the Lane Information window for each lane also shown at the top of the lane e Band IDs Letter and number combinations showing the lane letter and band position 83 Doc IT USER MANUAL number that uniquely identifies each band All of the above items can be turned on or off using commands in the View menu 1D Analysis submenu Context Menu Commands A context menu is a menu that appears when you click on the image itself with the right button of the mouse It is a shortcut menu that lets you sidestep using the menus or the toolbars Once you bring it up treat it as a regular menu by selecting features from the list The 1D Gel Image context menu contains the same commands as the standard context menu with the following additions e Lane Profile Gra
169. ve less than two calibrated lanes RETARDATION FACTOR RF LINES Automatic Rf Line Determination When you calibrate two or more lines with molecular weight standards Doc lt creates Retardation factor Rf Lines for you automatically These lines express any differences in horizontal alignment between bands or points on a lane of equal molecular weight There will be one Rf line for each distinct molecular weight used in a calibration Since you may use more than one standard on a single image and each standard may contain several weights automatic generation can result in a large number of Rf lines 92 Doc IT USER MANUAL You can remove an automatic Rf line by uncalibrating the lanes or by changing their calibration You can adjust an automatic Rf line by dragging the lane intercept marker up or down but only in lanes that are not calibrated To Adjust an Automatic Rf Line 1 From the 1D Analysis menu select Edit 1D Objects 2 If Rflines are not visible turn them on through the View menu From the View menu select 1D Analysis then turn on Rf Lines 3 Select the Rf line you wish to adjust Control handles will appear 4 Any lane that has a white control handle without an X is an uncalibrated lane and it is possible to move the intercept point up or down by dragging it If lane has a gray control handle with an X it is calibrated and cannot be moved 5 After you have adjusted Rf lines you may find it conveni
170. w Help Close All Tile Horizontal Tile vertical Cascade 15 vw 1 Colony tif zoom 100 Fa FA Fil Pl zb Doc IT USER MANUAL Help Menu Contains access to this Help system Help Digi Dac IE Help Fi About Fz Some commands have accelerator keys CTRL something that allow you to access the commands more quickly Virtually all commands can be placed on the toolbar through the Preferences window TOOLBARS The toolbars in Doc lt allow you to select most commands with a single button click The toolbars are completely customizable so you can include the commands you use most and remove commands you rarely use Initial Toolbar Buttons The initial buttons are Open Opens an image file on disk Save Saves the current image to disk Print Prints the current image Undo Reverses the last material change to the current image Cut Cuts selected text only Copy Copies selected text selected portions of the current image or the entire image to the clipboard Paste Pastes the current clipboard item into an appropriate part of the application View Capture Panel Hides or shows the Capture Panel View Annotations Hides or shows annotations on the current image View Rulers Hides or shows rulers on the current image Image Information Shows additional details about the current image Histogram Shows the Intensity Histogram window Effects Shows the Capture Panel if hidden a
171. will return to an image with no lanes or bands You also can access this feature using the toolbar or the shortcut menu on the Image window itself To Adjust Search Parameters If the basic search did not find all lanes you can adjust the parameters until the results are satisfactory To adjust the parameters 1 If you reopened the Lanes Bands dialog window or manually adjusted lanes ensure that Lanes and Bandes is selected in the search mode at the top of the window Otherwise the system will only search for bands within the existing lanes you have defined 2 Under Options select whether you want lane width to be constant across all lanes or for all lanes to be straight 3 Under Search Parameters check that the Image Background is correctly set If not change it to match the background Having the wrong background setting is the cause of most problems in finding lanes and bands Images with extraneous effects writing light leaks on the edges of the image sometimes cause background color to be detected incorrectly 4 Adjust the lane sensitivity using the slider control In general to detect more lanes drag the slider to the left to detect fewer lanes drag it to the right Sometimes however if the sensitivity is very low you may find more lanes and better defined ones by moving the slider to the right As you are changing Doc IT USER MANUAL sensitivity the image adjusts automatically You may also typ
172. y Band Peaks Band Extents Corrected Values or Background Correction 6 Under Print Options select if you want to Graph Using Color if not selected the printout will be black and white f Click OK A preview window of the report appears 8 Select Print To Change General Layout Before Printing 1 To change the title of the report as it appears on the printout type the new name at the top 120 Doc IT USER MANUAL 2 To change the margin size click on the drop down menu under Margins You can make the margins larger or smaller by varying degrees To view the margin lines select Draw Margin Lines 3 To change what appears in the Header Text or Footer Text note the following abbreviations for header and footer text e p puts the page number at the top or bottom of the page e c puts the page count at the top or bottom of the page e d puts the date at the top or bottom of the page e Sot puts the time at the top or bottom of the page 4 Click Refresh Preview near the top left of the window to effect the changes Related Topic Chapter 14 Finding Lanes and Bands 121 Doc IT USER MANUAL GLOSSARY Artifact In imaging a flaw caused either by the imaging process or by the hardware itself For example dust on the camera lens could cause small bright or dark spots in an image Aspect Ratio The ratio between an image s width and its height If the aspect ratio is not preserved the image will appear
173. ypically are stored in RGB or Red Green Blue Each color pixel therefore has three intensities the intensities of the red green and blue making up the pixel s color Some combinations result in different colors than one might expect For instance a color pixel with high red and green values but low blue values appears yellow On the other hand it is probably not very surprising that a pixel with high red values and low green and blue values appears red or that a pixel with high red and blue values but low green values appears purple The Meaning of Image Depth Intensity numbers are not fixed in size Different images and different image file formats support different sizes of intensity number The size of the intensity number is referred to as image depth Doc lIt supports 8 bit and 16 bit depth images This means that in Doc It an image may have either an intensity range from O to 255 8 bit or from O to 65535 16 bit 16 bit images have 42 Doc IT USER MANUAL considerably more granularity than 8 bit images Either way the intensity number range is per color channel Thus a 8 bit color image requires 24 bits or 3 bytes per pixel to store an 8 bit red an 8 bit green and an 8 bit blue value A 16 bit color image requires twice as much storage per pixel Displaying Depth Most color monitors and video cards today support 24 bit color there is also a 32 bit color mode but this is actually the same as 24 bit it just has

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