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OMERO clients User Guide - The Open Microscopy Environment

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1. 2 Projects Categories e tt Projects Categories zl AnotherDemoProject l H a AnotherDemaProject 0 P a DemoProject 2 a Sy cous z i estDatasetl 1 b Gj TestDataset 5 Figure 3 3 4 1 Project listing without Figure 3 3 4 2 Project expanded to show datasets datasets Copyright 2006 2007 University of Dundee All Rights reserved Page 31 OMERO clients User Guide 3 3 5 Expanding a dataset to see constituent images The number in brackets after a dataset name is the number of images belonging to that dataset To see all images belonging to a dataset click the Expand icon as above the images will now be listed Figure 3 3 5 1 t Projects Categories H p b E AnotherDemoProject E DemoProject 2 gt Gl TestDatasetl 10 v Gy TestDataset2 5 2 Test images 2 3461p 5dksub stk S Test images 654Avemp sik a Test images img R3D dv 3 Test images PA 505 RFP Cene 3 Test Images 72987_G1_BFO1_ Figure 3 3 5 1 Expanded dataset showing images The file path name shown in particular the number of directories preceding the filename reflects the settings specified when importing using OMERO importer See Section 2 3 for choosing display options for lists of image filenames Copyright 2006 2007 University of Dundee All Rights reserved Page 32 OMERO clients User Guide 3 3 6 The Projects Categories and Images tabs You will see that in
2. 1 Select the image or dataset for which you wish to see the annotations 2 Select the Annotation tab in the right hand pane 3 A window appears with two panes see Figure 3 6 2 1 e The left hand pane shows a tree list of all annotations for the selected image dataset or project plus date and time the annotation was made Annotations are grouped by users allowing you to see any annotations made by other users e The right hand pane provides an area for you to add a new annotation it also shows the content of all existing annotations You can also view an image s annotation s in the Image Viewer see Section 2 4 1 or in the Hierarchy Viewer see Section 3 10 Copyright 2006 2007 University of Dundee All Rights reserved Page 38 OMERO clients User Guide 3 6 2 Annotating a single image or dataset To add a new annotation to a selected image or dataset 1 Making sure the Annotation tab is selected type in a new annotation in the right hand pane 2 Oncompleting the annotation select the Save button to confirm On saving the annotation will be stamped with the user who created the annotation and the time the annotation was created ELELEE Peper Tempara k beage fle the eager felted dD bead 29 TL Le H T bi himi Seii F E J ore luih J Eoi T hia Faeroe ajio L peach aad Fs ene farg Il hea arora F avd HH Tanin meS 2 are ero F un arenes H 7 08 i bh T dea fi F 7 05 70 LLED Meg Daad T
3. Page 56 OMERO clients User Guide The Find in Tree feature can also work with datasets projects categories and category groups i e whatever is currently listed in the left hand pane Copyright 2006 2007 University of Dundee All Rights reserved Page 57 OMERO clients User Guide 3 9 Viewing images In Section 2 4 1 we described how you can view an image in constituent channels time points or z sections in OMERO s Image Viewer Section 2 4 2 described how thumbnails of a selection of images can be viewed using the Hierarchy Viewer This section provides further information on viewing images using the Image Viewer Bites EFaeertasen Fe io i Fans T Figure 3 9 1 The Image Viewer standard view 3 9 1 Viewing a specific Channel 3 9 2 Additional viewing options 3 9 2 1 Colour and greyscale viewing 3 9 2 2 Movie viewing across channels 3 9 2 3 Channel configuration 3 9 2 4 Image information 3 9 2 5 Annotation View 3 9 3 Magnification 3 9 3 1 Magnifying the whole image 3 9 3 2 Magnifying an area of the image 3 9 3 3 Scale bar 3 9 4 Viewing z sections and timepoints 3 9 4 1 Automated viewing of z sections and timepoints Copyright 2006 2007 University of Dundee All Rights reserved Page 58 OMERO clients User Guide 3 9 4 2 Selecting z section and timepoints 3 9 4 3 Additional Movie Player options for z section and timepoint viewing 3 9 5 lmage Rendering options Copyright 2006 2007 Universi
4. Inspector i Manager Results H P Feil Wale Text Text Show Text iw Show Measurements E Line Width 1 0 Font Size 10 0 Font Colour Fill Coleur Line Cobgur Measurement Text Colour io Loading Figure 3 10 5 4 1 ROI shape Inspector view To bring up the Inspector view adjust the appearance of an ROI shape 1 Select the ROI shape either by clicking on it in the Image Viewer window or by selecting it in the ROI Manager or ROI Results view 2 Select the Inspector tab 3 Current display settings for the ROI shape will be displayed 3 10 5 4 1 Adjusting display of annotation text 3 10 5 4 2 Adjusting display of the ROI shape 3 10 5 4 3 Hiding ROI shapes Copyright 2006 2007 University of Dundee All Rights reserved Page 105 OMERO clients User Guide 3 10 5 4 1 Adjusting display of annotation text The following adjustments can be made to the ROI shape s annotation text e Click the Show Text checkbox to turn on off annotation text e Click the Show Measurements checkbox to turn on off measurement text e Change the size of the annotation text by selecting the Font Size menu and selecting the appropriate value Copyright 2006 2007 University of Dundee All Rights reserved Page 106 OMERO clients User Guide 3 10 5 4 2 Adjusting display of the ROI shape The following adjustments can be made to the appearance of the ROI shape itself e Change the width of the ROI shape s line by selecting the Line W
5. and select an ROI shape by clicking on it e To select multiple ROI shapes hold down the Shift key while clicking ES Memurement Too lees dave Deteiog usable image Tesi Images img Rind i i an BM olole N N mia a Manager Inspector al Results EE Graph Pane i a Intensity View RON iD T F Type ARNOT visible ES ve i wa Ba T ivf T i r T Some text here cal isi 2 oo 1 3 l 2 ka if 1 F ba Z lE 3 E Ready Figure 3 10 5 1 1 ROI Manager window For more on editing ROIs groups of ROI shapes see Section 3 10 5 6 Copyright 2006 2007 University of Dundee All Rights reserved Page 98 OMERO clients User Guide 3 10 5 2 Annotation and labelling You can add a text annotation to an existing ROI shape or label an area of the image directly by adding a text ROI 3 10 5 2 1 Annotating an existing ROI shape 3 10 5 2 2 Labelling Images Copyright 2006 2007 University of Dundee All Rights reserved Page 99 OMERO clients User Guide 3 10 5 2 1 Annotating an existing ROI shape Separate to text ROIs an existing ROI shape can be annotated in one of three ways 1 Double click on the shape you can either edit the current annotation text or add new ones 2 Use the ROI Manager i Open the ROI Manager ii Select the shape to be annotated the selected ROI shape will be highlighted iii Type the annotation the annotation will appear as you type in the Annotation column iv The ann
6. 3 10 2 The Measurement Tool interface cccsssssseeeeeeeeeeeeeeeeeeeeeees 85 3 10 3 Creating ROIS ccicicsccansianenanaccnnsnsiiewawsdsnsnsnneisaensintinnsandslianenehsncwanaiianuiny 86 3 10 31 What is am ROI oriasi naaien asarei in aian 87 3 10 3 2 Creating a Single Shape ccccceeseseeeeeeeeeeeseeeeceeeeeeenneeees 88 3 10 3 3 Adding multiple ROI shapes on one plane ccssssseee 90 3 10 3 4 Creating an ROI across z sections and timepoints 91 3 10 4 Saving and loading ROIS vsisiisasinsiinacerssassnasvesamntiunsiciniivediinesaunins 94 3 10 41 Saving POI G vic thanai sccacssncnascdsniinceanesusninaciatetasuiaasnaisenmeaciiadsaiaiaiaes 95 3 10 4 2 Loading ROIS sssrinin rai sirnani 96 3 10 5 Editing ROIS isssisisnicannuii nrinn eraai a aa iiaia 97 3 10 51 Selecting ROIS srci aa 98 3 10 5 2 Annotation and labelling cccsssessseeeeeeeeeseeeeeeeeeesseeeeneeees 99 3 10 5 2 1 Annotating an existing ROI Shape cccssssssseeeeees 100 3 10 5 2 2 Labelling IMAGES sisisitisascisntinetinesniiinstivnerseneiionitnineniiin 101 3 10 5 3 Moving or resizing a single ROI ssunnnnsnnunnnnnnnnnnnnnnnnnnnnn 102 3 10 5 3 1 Moving a single ROI shape ccssssseeeeceeeeeeeeeeeeeeeees 103 3 10 5 3 2 Resizing a single ROI Shape sssseeeeeeeeeeeeeeeeeeeeees 104 3 10 5 4 Changing the appearance of an ROI shape 0 10 105 3 10 5 4 1 Adjusting display
7. 2006 2007 University of Dundee All Rights reserved Page 109 OMERO clients User Guide 3 10 5 6 Editing multiple ROI shapes and ROIs You can select whole ROls including all constituent ROI shapes or selected ROI shapes for editing 1 Right click on the ROI Manager 2 Select ROI Management Options This gives access a menu that allows you a number of options e Duplicate the selected ROI or ROI shape A copy of the selected ROI or ROI shape will appear in the ROI Manager as a new ROI e Merge two selected ROls with constituent ROI shapes into a single ROI e Split removing selected ROI shapes from their parent ROI and putting them into a new ROI e Propagate propagating the selected ROI or ROI shape as described in e Delete the selected ROI or ROI shapes Copyright 2006 2007 University of Dundee All Rights reserved Page 110 OMERO clients User Guide 3 10 6 Viewing ROI information A range of information relating to the ROI shapes present in the selected image can be viewed 3 10 6 1 Viewing summary ROI information 3 10 6 2 Measurement results 3 10 6 2 1 Showing summary results 3 10 6 2 2 Refreshing summary data 3 10 6 2 3 Saving summary data 3 10 6 3 Viewing pixel intensity values 3 10 6 3 1 Graphical view 3 10 6 3 1 1 Configuring the Graph view 3 10 6 3 1 2 Saving graphical views 3 10 6 3 2 Intensity View Copyright 2006 2007 University of Dundee All Rights reserved Page 111 OMERO clients
8. Figure 3 3 5 1 above the left hand pane there are two tabs Projects and Categories visible plus an arrow tab p a There should in fact be three tabs the hidden one is the Images tab If you only see two tabs clicking on this tab gives you a menu showing all three options allowing you to select the Images tab Alternatively hold down the mouse pointer in the space between the left and right hand panes and drag to the right to widen the left hand pane until all three tabs appear as in Figure 3 3 6 1 The arrow tab is reversed when only the Categories and Images tabs are shown i p In this case click the tab to access the Projects tab The Images tab is discussed further in Section 3 7 and the Categories tab is discussed further in Section 3 8 a eM Projects 1 Categories o Images T 23 David Sloan H J Orphaned Datasets 4 mj China 1 T Gg Tsingtao 2 E Test lmages 654Atemp stk gl Test images img_R3D dv i South America 1 E Brazii 18 El tubhiswt 40 tubhiswt_cC2_TP 1 gl Mbhiswt 4 Dubhs C2 TPL El tubhiswt 40 tubhiswt_C2_TP 1 gl tubhiswt 4D tubhiswt_C2_TP1 El tubhiswt 40 tubhiswt_C2_TP1 7 Figure 2 3 6 1 Expanded left hand pane showing three tabs Copyright 2006 2007 University of Dundee All Rights reserved Page 33 OMERO clients User Guide 3 4 Viewing other people s images OMERO supports collaborative work by allowing users to share i
9. Viewer viewing multiple images cccsssseeeee 124 3 11 1 Viewing an image from the Hierarchy Viewet sseee 126 3 11 2 Using the Hierarchy Viewel cccccsssescccecessssseeseeeeeeeeeesseeeeeees 127 3 11 2 1 Adjusting thumbnail display ccccsseeeceeeeeesseeeeeeeeeeees 128 3 11 2 2 Display Tree View Of images ccccccsssseeeeeeeeeseseeeeeeeeeeeeees 131 BT 12 55 Sorting iMageS o oxcicnssandenstcnenepssansdunsrsadeansensmansnansiannenwdcennansuanans 132 3 11 2 4 Managing images in the Hierarchy Viewet 00 s10 133 3 11 2 5 Additional image information the Working Area 134 3 12 Managing windows in OMERO insight ccccesssseeeeeeeeeeeeeeeeees 136 3 13 Closing OMERO INSIQIU siseiiisiecicieiccstsasdeadssitesieieeardiaadaanaeskieticndivedons 137 Ay Feedback reporting iseic niaiserie a aasian 138 4 1 Help Informati n saat ccctacticesacanstreratanccaiciniasudeacttintarnceuwiianacencebedianaeaaans 139 4 2 Feedback Facillty sireisas nian r riria 140 5 Background iMf rmati r saiiisisissininasinsenacedensnadacinsnsnadunniiandannanidiennensisetanianiases 141 Sil What iS OMERO saiae aniani aa aeaaaee aie 142 Copyright 2006 2007 University of Dundee All Rights reserved OMERO clients User Guide 5 2 The OMERO Environment client and Serve 2 2 c0s eeeceeeceeceeeseeeees 5 3 5 Dimensional IMAGES ccceeeeeeeeeeeeeeeeeeeees 5 4 The OMER
10. ordinates of the ROI The x y values for the end co ordinates of the ROI The x y values for all constituent co ordinates of the ROI The specific data values displayed in the Results view can be configured by selecting the Results Wizard button see Figure 3 10 6 2 1 It may be necessary to use the scrollbar to reveal all columns of data alternatively the window can be resized to show all data Jaqsurement Tool Users idie Desktopi usable image Test images img APD l Wms Molol ea Manager nd paeceor ecules H Graph Pane A iataniity Vire Lat T E Tret Anatamani Coriri Contreif Arra Lisjth WHR Figh Angr 1 3 Text Some te 1 l Eliisa aT BEF PEE BL FI FJ i 2 Elipsa af 432 2843 50 BL TL FJ 1 J Ellipse Lt LEF 4236 01 76 7l Results Wizard Refresh Save a Bead Figure 3 10 6 2 1 1 Results view Copyright 2006 2007 University of Dundee All Rights reserved Page 114 OMERO clients User Guide Copyright 2006 2007 University of Dundee All Rights reserved Page 115 OMERO clients User Guide 3 10 6 2 2 Refreshing summary data If any changes are made to the image s ROls for example by resizing them adding new ROI shapes or deleting existing ROI shapes the data shown in the Results view will not be displayed unless being refreshed through the Refresh button Copyright 2006 2007 University of Dundee All Rights reserved Page 116 OMERO clients User Guide 3 10 6 2 3 Saving summary data To sav
11. play all z sections or timepoints in sequence as a movie Alternatively Holding down the mouse button and dragging the mouse vertically up or down the image moves through z sections dragging horizontally moves through timepoints Dragging diagonally will simultaneously change z sections and timepoints For more details on viewing z sections and timepoints using the Movie Player see Section 3 9 4 Copyright 2006 2007 University of Dundee All Rights reserved Page 12 OMERO clients User Guide 2 4 1 2 Adjusting channels To adjust channels for multi channel images in the Image Viewer Standard View or Split View e Use the colour buttons on the left hand side of the image to turn on or off a colour channel e Switch between colour and greyscale representations of the image by going into the Controls menu selecting Models and choosing Colour or Greyscale For more details on adjusting channels see Section 3 9 Copyright 2006 2007 University of Dundee All Rights reserved Page 13 OMERO clients User Guide 2 4 1 3 Additional viewing options The Image Viewer provides a number of additional tools Adjust the image properties using the Rendering Tool see Section 3 9 3 5 Magnify an image or area of interest within the image see Section 3 9 3 View in greyscale or view additional information about the image see Section 3 9 2 Configure the optional scale bar see Section 3 9 3 3 Copyright 2006 2007 U
12. saved for exporting to other applications Measurement Tool Users davesDeskiops ule mage lest Images img APG dy ai fas T ololelNNIn ea 3 Manages L inepeetor L L Results TH Graph Pane batencsiey wow z TSS EET Tye Anmam Centre Gemeet Area Length With Regt Angie 1 i 3 Text Some te I 1 Elippe a LEFI 7543 93 BL Fl rd i 2 Ellipse aF aii 7643 93 GL Fi Z 1 J Ellipse oo 432 4238 01 76 Fl Results Wizard 4 Refresh J Save EP Beachy Figure 3 10 6 2 1 Results view 3 10 6 2 1 Showing summary results 3 10 6 2 2 Refreshing summary data 3 10 6 2 3 Saving summary data Copyright 2006 2007 University of Dundee All Rights reserved Page 113 OMERO clients User Guide 3 10 6 2 1 Showing summary results The data displayed by default in the Results view includes Unique ID of the ROI shape The T section in which the ROI appears The z section in which the ROI appears Type of ROI shape Annotation text The x and y co ordinates of the centre of the ROI The area of the ROI if a rectangle ellipse or polygon in square microns or pixels depending on the units specified in the Options menu The length of the ROI if a line The width and height of the ROI if a rectangle ellipse or polygon e The angle of the ROI from the horizontal if a line In addition it is possible to view The length of the perimeter of the ROI if a rectangle ellipse or polygon The x y values for the start co
13. the default rendering settings are not the ones previously saved but the internal defaults of the rendering facility Copyright 2006 2007 University of Dundee All Rights reserved Page 81 OMERO clients User Guide 3 10 Introduction to the Measurement Tool The Measurement Tool significantly extends the functionality of the Image Viewer by allowing you to perform a variety of measurement tasks and analyses on your image These include e Defining Regions of Interest ROIs on the image and on each z section or timepoint of multi dimensional images e Annotating ROIs with textual annotations e Assigning stroke and fill colours to shapes e Getting measurements of the ROI shapes including area length and angle e Plotting intensity values e Loading existing ROIs and saving ROls to file and e Managing ROls editing shapes viewing deleting and adding Liars Wem Fieri yi Hele Central renr CSN i Pl a tee tom wee ats BB olola s n a a vee Aseceuicon i hepa Masiger O Mraults FE Tarii oor a Loading 4 T 3 4 T 0 d Figure 3 10 1 Image Viewer with Measurement Tool 3 10 1 Accessing the Measurement Tool 3 10 2 The Measurement Tool interface 3 10 3 Creating ROIs 3 10 3 1 What is an ROI Copyright 2006 2007 University of Dundee All Rights reserved Page 82 OMERO clients User Guide 3 10 3 2 Creating a single shape 3 10 3 3 Adding multiple ROI shapes on one plane 3 10 3 4 Creating an ROI acros
14. to remove this pane Copyright 2006 2007 University of Dundee All Rights reserved Page 131 OMERO clients User Guide 3 11 2 3 Sorting images Like the Data Manager images in the Hierarchy Viewer can be sorted within a set by date or name see Section 3 8 1 13 Alphabetical sort Select this option to sort image file names in alphabetical order cr Date sort Select this option to sort image file names in order of the date they were taken on the microscope and if this information is not available in order of the date of import into OMERO Copyright 2006 2007 University of Dundee All Rights reserved Page 132 OMERO clients User Guide 3 11 2 4 Managing images in the Hierarchy Viewer In the Hierarchy Viewer you can perform management actions on a single image or multiple images Categorise or decategorise an image or selection of images View and edit annotations for an image or selection of images View property information of an individual image Remove an image from its current dataset To perform any of these tasks you can e Select one or more images in a container and then open the Edit menu to select the operation of your choice e Or right click on a single image to see the Edit menu as above Icons are used to indicate the presence of category and annotations for any image appearing as a thumbnail in the Hierarchy Viewer this iconic information is preserved for pinned up thumbnails Cl
15. ts Projects t amp Categories H p 3b z Y amp Jean Marie Burel 3c gt Orphaned Datasets 14 Y E Elite Project 1 gt S test create 2 gt E project one 2 gt E test 2 Figure 3 1 1 Data Manager default screen with three projects listed If you wish to send a comment to the OMERO development team open the Help menu and select Send Comment Copyright 2006 2007 University of Dundee All Rights reserved Page 22 OMERO clients User Guide 3 2 Viewing and editing user account details You can make a limited amount of changes to your OMERO account details in the Data Manager At the top of the tree in the left hand pane of the Data Manager is your own user name Click on this to see your user account details shown in the right hand pane see Figure 3 2 1 There are two tabs My Profile snows basic personal information e My Servers shows all OMERO servers for which you have a user account irral hasir s bala M Etairiate yy Pret C magara b Profa liter a 7 Lede iy Pepe Lp ul Hih S Pii Disi jaa E J rd Dauerh F LA hy Prig l Vp rrura ai Cein T Tengu LE Merri Horse Dred a Tan maputlang Th E Tau kapa img Aid Lari Meraq oe Fp tas areca b baad ih Lomed nan ee ng eee ae rh Yh Cartas jj indi Les y of Denies E eet aj kapha a Drisas B rma pa aj pip eL 5 k i Fj bai LT ed Wr eae Aaa aj miian Dna CE Ej ubhman i Di L T Bj narra ivn E T Od pureed ee a i E Ej bi
16. you will be able to set permission levels for accessing the selected project dataset or image see Figure 3 5 1 e The Annotations tab allows you to see and add annotations to the selected dataset or image You cannot add an annotation to a project For more on Annotations see Section 3 6 e The Info tab is available when an image is selected This provides information about the image including X Y dimensions number of z sections and timepoints pixel sizes and number of emission wavelengths be fan be aajt kikii ii nkk CL THT T haia Fate j it i mad titg EEEE PEE Dede Come Denar Grma 7 Figure 3 5 1 Viewing permissions information for a selected image Copyright 2006 2007 University of Dundee All Rights reserved Page 36 OMERO clients User Guide 3 6 Annotations OMERO lets you add annotations textual notes to any image or dataset in your collection You can also add annotations to any other images that you have permission to see 3 6 1 Viewing annotations 3 6 2 Annotating a single image or dataset 3 6 3 Annotating multiple images or datasets Copyright 2006 2007 University of Dundee All Rights reserved Page 37 OMERO clients User Guide 3 6 1 Viewing annotations The ET icon shows that a dataset has one or more annotation see TestDataset1 in Figure 3 3 4 1 for an example The gj icon shows that an image has one or more annotations To view annotations in the Data Manager
17. EA Add a new dataset to project project one Y project one 2 gt eT dataset one 1 gt E dataset three gt 5 test 2 Name Description Figure 3 3 1 3 Adding a new dataset to an existing project Copyright 2006 2007 University of Dundee All Rights reserved Page 27 OMERO clients User Guide AAO Jean Marie Burel s Data Manager File Edit View Window Help OEA S a BSS W Projects tz Categories u ara Dataset Edit the dataset test create F Seo er Properties Annotation Y Jean Marie Burel gt Orphaned Datasets 13 E Elite Project 1 gt S test create 2 gt E ffff 1 ID 111 gt ima project one 2 a Name est create gt E test 2 Description Owner Jean Marie Burel E mail j burel dundee ac uk Figure 3 3 1 4 Data Manager showing one available project containing one dataset Copyright 2006 2007 University of Dundee All Rights reserved Page 28 OMERO clients User Guide 3 3 2 Renaming projects or datasets To rename a project or dataset 1 Select the project or dataset 2 Inthe right hand pane edit the text in the Name field 3 Select Save to confirm changes Copyright 2006 2007 University of Dundee All Rights reserved Page 29 OMERO clients User Guide 3 3 3 Removing projects or datasets To remove a project or dataset 1 Inthe left hand pane of the Data Manager select the proje
18. Figure 3 10 3 2 3 Elliptical shapes shape showing ROI shapes length and angle detail and connector line Copyright 2006 2007 University of Dundee All Rights reserved Page 89 OMERO clients User Guide 3 10 3 3 Adding multiple ROI shapes on one plane There is an option to allow to quickly add many ROI shapes of the same kind on the same image plane e To move to multiple addition mode open the Options menu select ROI Creation and then select Create Multiple ROIs which allows you to add many ROI shapes e When you have finished adding shapes click the Selection button to select an ROI shape e To return to single addition mode open the Options menu select ROI Creation and then select Create Single ROI Alternatively you can toggle between single and multiple addition mode by right clicking on the ROI shape format button before adding a shape of that format This will allow you to add multiple ROI shapes of the selected format To move from multiple addition mode to Selection mode you will have to click the Selection button as above Copyright 2006 2007 University of Dundee All Rights reserved Page 90 OMERO clients User Guide 3 10 3 4 Creating an ROI across z sections and timepoints ROI shapes once drawn on a single plane can be propagated copied across multiple z sections or timepoints to create a multi dimensional ROI To propagate an ROI shape 1 2 3 gt A o Og Select the ROI
19. I An ROI across multiple dimensions z sections or timepoints will be created when an individual ROI shape is selected and propagated Propagating ROI shapes to create multi dimensional ROIs is discussed more in Section 3 10 3 4 Viewing and managing ROIs and ROI shapes is discussed more in Section 3 10 5 and in Section 3 10 3 6 Copyright 2006 2007 University of Dundee All Rights reserved Page 87 OMERO clients User Guide 3 10 3 2 Creating a single shape To create a single ROI shape on a single plane z section or timepoint on an image select the appropriate toolbar shape option and draw the shape To draw a rectangle 1 Select the Rectangle toolbar button 2 Hold down the mouse button on one corner of the area you wish to form the ROI and drag to the opposite corner 3 Release the mouse button the rectangle is now created To draw an ellipse 1 Select the Ellipse toolbar button C 2 Click on the edge of the area you wish to form the ROI and drag the mouse pointer until the circular shape approximates the ROI you wish to produce 3 Release the mouse button the ellipse is now created To draw a circular point for example for counting spots 1 Select the Point toolbar button E3 Click on the area of the image you wish to mark The point is now created see Figure 3 10 3 2 1 for an example of multiple points drawn on an image N To draw a straight line 1 Select the Line toolbar bu
20. MERO clients User Guide 3 9 4 Viewing z sections and timepoints For images with multiple z sections and or timepoints the Image Viewer can allow manual or automated viewing of each section Z sections and timepoints can be viewed separately or together 3 9 4 1 Automated viewing of z sections and timepoints 3 9 4 2 Selecting z section and timepoints 3 9 4 3 Additional Movie Player options for z section and timepoint viewing Copyright 2006 2007 University of Dundee All Rights reserved Page 73 OMERO clients User Guide 3 9 4 1 Automated viewing of z sections and timepoints In Section 2 4 1 1 we outlined how the z section or timepoint being viewed can be manually configured using the sliders provided by the Image Viewer You can also view each of the image s composite z sections or timepoints as a movie Each z section or timepoint is displayed in sequence for a short time period to form the movie A D Movie Player 041206_3HT3_stain B Play Forward HH fe Across pales ue 2 Start End 63 Fe Start End Figure 3 9 4 1 1 Movie Player To play z sections or timepoints as a movie 1 oy ge ee In the Image Viewer window e Either select the Play Movie button fe e Oropen the Controls menu and select the Movie option The Movie Player window appears Figure 3 9 4 1 1 Select the Play button gt to play the movie Select the Stop button H to stop the movie When a movie is playing the Play bu
21. O Data Model and Hierarchies Copyright 2006 2007 University of Dundee All Rights reserved OMERO clients User Guide 1 Introduction Welcome to OMERO This document provides a comprehensive guide to the Beta version of the OMERO importer and OMERO insight These applications together allow you to import your microscopy images into the OMERO system and manage manipulate and view them The software was released for general use in June 2007 This guide includes the following sections Section 2 Getting started with OMERO Installing the software and a brief guide to importing images using OMERO importer and performing basic image management viewing and manipulation tasks using OMERO insight Section 3 Advanced OMERO More details on using OMERO insight Section 4 Help and feedback How you can provide the development team with feedback to influence future development Section 5 Background information The concepts and models behind the OMERO suite of software Enjoy using the software The OMERO development team University of Dundee UK Copyright 2006 2007 University of Dundee All Rights reserved Page 1 OMERO clients User Guide 2 Getting started with OMERO This section provides you with the essential information you need to perform key tasks using OMERO Installing the software Logging in Importing images Viewing single multiple image s Annotating images Saving images More ad
22. OMERO clients User Guide ROI Assistant The ACW Assistant allows you to create an RON which extends aR through time and sections oe E Add ROI 4 C Remowe ROI 1 0 2 O O Shape Type Ellipse X Coord 100 6 Width ETT Description Text Y Coord 220 0 Height 74 0 Close Figure 3 10 3 4 2 Propagating ROI shapes selecting z sections as propagation destinations Copyright 2006 2007 University of Dundee All Rights reserved Page 93 OMERO clients User Guide 3 10 4 Saving and loading ROIs ROI data need to be saved manually in order to be able to recall it in future This is because ROls and associated date are saved separately to the image itself and ROI information is currently not saved automatically in OMERO 3 10 4 1 Saving ROIs 3 10 4 2 Loading ROIs Copyright 2006 2007 University of Dundee All Rights reserved Page 94 OMERO clients User Guide 3 10 4 1 Saving ROIs The following adjustments can be made to the ROI shape s annotation text e Select the Save button fal e Choose the location for the saved ROI file using the file browser window that appears e Select Save If you try to close the Image Viewer with unsaved ROI information a prompt will ask you whether or not you wish to save this information Copyright 2006 2007 University of Dundee All Rights reserved Page 95 OMERO clients User Guide 3 10 4 2 Loading ROIs To view ROls associated with an image 1 Open the
23. Open Microscopy Environment Project Open Microscopy Environment Authors David Sloan Xinyi Jiang Jean Marie Burel Donald MacDonald Brian Loranger Version 3 0 Beta 2 2 Date 2007 11 05 OMERO clients User Guide open microscopy environment Copyright 2006 2007 University of Dundee All Rights reserved OMERO clients User Guide Table Of Contents Ds MNO OO ses EE EA A A A EEE 1 2 Getting started with OMERO sincsicssnisintiinnssecatiestaviansinnd tan ennaii neidr aaien 2 2 1 Installing OMERO importer and OMERO insight ccccessssseeeeees 3 22 LLOQ GING Mirisi aaa AOAR EEr ara Aasa pi 4 2 3 Importing IMAGES sitsciccntssidisidcnssnrisnniieasinadansdcetinnianncantiasniiamanaiiaishaananidireens 5 2 4 WICWING IMAGES siiani inea aaaeeeaa aerae aai aico i areais 9 2 4 1 Viewing a single iMage ssssnnnsssnnnnnnnennnnnnnnnennnnnnnnnnnnnnnnnnnnn nnmnnn nna 10 2 4 1 1 Viewing z sections or tiMePOINHS seeccceeeseeeeeeeeeeeeseeeeeeees 12 2 4 1 2 Adjusting CHANNEIS isiisnrsiessnciesesaninipiediorienaseniaidiiircindieenianies 13 2 4 1 3 Additional Viewing Options cccccssseeeeeeeessseeeeeeeeeeeseenneeeees 14 2 4 2 Viewing a selection of images the Hierarchy Viewet 15 2 5 SAVING MAJ S ees sisresnencanessansnducacannendeensaaisndnstkah anensudianaancdeadevitetaniadianain 17 3 Advanced OMERO sass eicericcctescectes aeaniee tae osaa ian ian anisa 18 3 1 Getting to know the Da
24. Select the saved image file format from a choice of BMP JPEG TIFF or PNG d Choose the type of image to save in the Images menu select from A simple image Image and split channels in grid form Image and split channels in a row Image and split channels in a row in grey Lens image Lens image and split channels Lens image and split channels in grey 3 You will see a preview of the image to be saved before you confirm the save action Copyright 2006 2007 University of Dundee All Rights reserved Page 17 OMERO clients User Guide 3 Advanced OMERO This section provides more in depth information on the tasks OMERO insight supports 3 1 Getting to know the Data Manager 3 2 Viewing and editing user account details 3 3 Managing projects and datasets 3 3 1 Creating projects and datasets 3 3 2 Renaming projects or datasets 3 3 3 Removing projects or datasets 3 3 4 Expanding a project to see constituent datasets 3 3 5 Expanding a dataset to see constituent images 3 3 6 The Projects Categories and Images tabs 3 4 Viewing other people s images 3 5 Additional information about projects datasets and images 3 6 Annotations 3 6 1 Viewing annotations 3 6 2 Annotating a single image or dataset 3 6 3 Annotating multiple images or datasets 3 7 Categorising images 3 7 1 Creating category groups 3 7 2 Creating categories 3 7 3 Removing categories and category groups 3 7 4 Categorising images 3 7 4 1 Categorising a singl
25. Single wavelength 20 stack Mi oa go 20 irmas Single wanah 2D Limalapeo A nw Sigh wavdlengin 20 hana Iram GED oe kikii sear Figure 5 3 1 Multiple dimensional images Copyright 2006 2007 University of Dundee All Rights reserved Page 144 OMERO clients User Guide 5 4 The OMERO Data Model and Hierarchies All information in OMERO revolves around a data structure called the object hierarchy An understanding of this is core to efficient and effective use of OMERO This hierarchy defines three kinds of objects 1 Projects 2 Datasets 3 Images and an organisational structure for grouping these objects together This structure is shown in Figure 4 4 1 Project Datasets Figure 5 4 1 OMERO Object hierarchy At the top of the object hierarchy is the project Projects represent a large long term investigation usually by either a single OMERO user or a small collection of users in the same research group Each project contains a number of datasets Projects and datasets form a many to many relationship a project can contain more than one dataset and each dataset can belong to more than one project Most analysis routines are performed at the dataset level This provides both a convenient batch processing capability and the ability to calculate aggregate information about the contents of a dataset Each dataset contains a number of images Like projects images form a many to many rela
26. User Guide 3 10 6 1 Viewing summary ROI information A summary information for all ROls of an image can be revealed by clicking on the Manager tab All ROls and constituent ROI shapes are listed see Figure 3 10 5 1 1 indicates an ROI e 7 indicates an ROI shape For each ROI ROI shape the following essential information is shown e For ROls all constituent ROI shapes this will be the case where an ROI shape has been propagated across z and or t to create a multi dimensional ROI e The unique ID number of the ROI ROI shape e For ROls the timepoints and or z sections across which it exists e The type of ROI shape one of Rectangle Ellipse Point Line Connector Polygon or Text is indicated by the appropriate symbol e Annotation text e Whether or not the ROI ROI shape is currently visible To adjust the amount of data shown in the ROI Manager the display can be adjusted in the following ways e ROls can be expanded to show constituent ROI shapes by clicking on the grey Expand arrow to the left of the ROI e Tocollapse an expanded ROI select the grey Collapse arrow Copyright 2006 2007 University of Dundee All Rights reserved Page 112 OMERO clients User Guide 3 10 6 2 Measurement results The ROI Results View shows summary measurement results for all ROIs and ROI shapes see Figure 3 10 6 2 1 It also allows you to configure which data should be included in any resul data file to be
27. aa CFF Siem pirinin aj le iD Ei OF Tonina piri aj ppap LT Sj ih LET Charge canieced a Or Figure 3 2 1 User Profile Editor The only edits you can make at present is to change your OMERO password using the form here Future releases of OMERO will allow you to make additional changes to your account which currently can only be made by users with OMERO administrator status The ability to change from one server to another will also be added in future versions Copyright 2006 2007 University of Dundee All Rights reserved Page 23 OMERO clients User Guide 3 3 Managing projects and datasets In Section 2 3 we explained how to create projects and datasets as part of the Import process OMERO insight also allows you to create and manage projects and datasets The following icons are used in OMERO insight e ml denotes a project e SD denotes a dataset e E denotes an image 3 3 1 Creating projects and datasets 3 3 2 Renaming projects or datasets 3 3 3 Removing projects or datasets 3 3 4 Expanding a project to see constituent datasets 3 3 5 Expanding a dataset to see constituent images 3 3 6 The Projects Categories and Images tabs Copyright 2006 2007 University of Dundee All Rights reserved Page 24 OMERO clients User Guide 3 3 1 Creating projects and datasets To create a project in OMERO insight 1 2 3 4 In the File menu select Create New project Or select the ay icon In t
28. ally or as a selection of thumbnails When you first log in to OMERO insight you will see the image filenames listed under the relevant Project and Dataset in OMERO insight s Data Manager see Figure 2 4 1 See Section 3 1 for a fuller description of the Data Manager areal thts hela Marae at ie HT a T Feier Conger 3 beage dA ibe bragr heen deve Cerra hep Tari brg irag i S hs H Tii i aa E D per uih jE i C Ib T hmin F Amaia j io TE Tenas F PENERE eee i ages aay T d Gavel Pae l eee eed a a i ew ea Ei Te ee eee 27 25 17 RARI a7 05 07 ERE ahi thin geri u u pu pa Gu a me aana An Mja Emai aami Figure 2 4 1 Data Manager Window showing images stored in OMERO 2 4 1 Viewing a single image 2 4 1 1 Viewing z sections or timepoints 2 4 1 2 Adjusting channels 2 4 1 3 Additional viewing options 2 4 2 Viewing a selection of images the Hierarchy Viewer Copyright 2006 2007 University of Dundee All Rights reserved Page 9 OMERO clients User Guide 2 4 1 Viewing a single image To view an image e Either double click on the image filename e Or select the image filename and then select the View Image button mj In either case the image will be displayed in a new window the Image Viewer window The Image Viewer allows you to view your image in three different ways e Standard Image View see Figure 2 4 1 1 e Annotation View reduced size image with details of annota
29. aninensdesciniaaiananiinnsan 43 3 7 2 Creating CALC GOMES cecaiisccsaseccnnensionavsdsdincenensanesinidansandlianenebsacwsnniiananns 44 3 7 3 Removing categories and category Groups ccceeeeeeeeeeeeeeees 45 3 1 As CALCGONSING IMAGSS isistesitsmanscetestscssamaniontesiansiad usieandianannededidvdeanayinbiandan 46 3 7 4 1 Categorising a single image cccsseseeeeeeeeeeeeeeeeeeeeeseeeeeeees 47 3 7 4 2 Categorising Multiple iMaGeS ccccssseeeeeeeeeeeeeeeeeeeeeeeeeeeees 48 3 7 4 3 Viewing images in a CATCCOLY ccceeeeeeeeeeeeeeeeeeeeeeeeenseneneeeees 49 3 7 4 4 Removing an image from a CateQOLy scccccsseseeeceeeeesssseeeeeees 50 3 8 SOMING and finding IMAGES sissies cciecsisssiassdscecndentntindvissandacteerinstenanuaes 51 3 6 1 SOMING IMAGES isisisi anaa aa auriei aana na RluaNiE 52 3 8 2 Retrieving selected images cccccssseeeeceeessseseeeeeeeeeeeeeeeeeeeeeeeeees 54 3 8 3 Finding images with Find in Tree cccsssssseeeeeeeeeeeseeeeeeeeeees 56 3 9 Viewing IMCS viiicrccsctccnesisdsnsnsacnrnenseennuniandusncabsaneedusianaantdaneanntetaniadawnnens 58 3 9 1 Viewing a specific Channel ccccccssseeseceeesssseeeeeeeeeeessseeeeeeeeees 60 3 9 2 Additional viewing OptiONns ccccssseeeeeeeeessseseeeeeeeeeeeeeeeeeeeeeeeees 61 3 9 2 1 Colour and greyscale viewing ss sseeceeeeeeseeeeeeeeeeeeneneeeeees 62 3 9 2 2 Movie viewing across channels sssssssssss
30. ars choose which channel to adjust The Colour Picker window opens Figure 3 9 2 3 1 You can then select a colour in one of three ways each available by selecting one of the toolbar buttons at the top of the window These options are SN a Using the HSV colour wheel b Using RGB colour sliders shown in Figure 3 9 2 3 1 c Showing the colour list 5 Once happy with your settings select Accept to confirm the changes or Revert to ignore the setting changes you have just made 6 You should now see the channel change applied to the relevant channel button Colour Picker Window AP Channel info Lo Channel Info Edit the selected chan Q Emission Wavelength in p 457 a Mg a Excitation Wavelength in p 457 Green nnee ND Filter 1 0 255 Pin hole size i Blue ie t A m 255 GRD Cat Ge Figure 3 9 2 3 1 Colour Picker Figure 3 9 2 3 2 Channel Info window The Colour Picker can also be accessed by double clicking on a channel button Right clicking on a channel button gives access to a menu from which you can choose to bring up the Colour Picker or to display additional information about the channel Figure 3 9 2 3 2 Copyright 2006 2007 University of Dundee All Rights reserved Page 64 OMERO clients User Guide Copyright 2006 2007 University of Dundee All Rights reserved Page 65 OMERO clients User Guide 3 9 2 4 Image information To view basic information ab
31. at group similarly the number after each category name indicates how many images belong to that category 4 Projects amp Categories EE Images l OOMS J Orphaned Categories 1 7 i 13th December 2 Haugesund 0 H Stavanger 3 T GD 22nd May 2 Mo i Rana 0 Narvik 0 Figure 3 7 2 1 List of category groups with categories Copyright 2006 2007 University of Dundee All Rights reserved Page 44 OMERO clients User Guide 3 7 3 Removing categories and category groups To remove a category from a category Group 1 Select the category to be removed 2 Inthe Edit menu select Remove 3 The category will be removed from the category group Orphaned Categories will be created to hold the removed category 4 The removed category will go to Orphaned Categories which appears on top of the tree view The number in the bracket shows how many removed categories are in 5 Similarly to remove a category group select the category group to be removed and use the Edit menu as above A category or category group is only removed from a project it is not deleted from the system Copyright 2006 2007 University of Dundee All Rights reserved Page 45 OMERO clients User Guide 3 7 4 Categorising images Once you have created one or more categories you can categorise your images 3 7 4 1 Categorising a single image 3 7 4 2 Categorising multiple images 3 7 4 3 Viewi
32. ave button Copyright 2006 2007 University of Dundee All Rights reserved Select the Save as option in the menu that appears Page 121 OMERO clients User Guide 3 10 6 3 2 Intensity View Selecting the Intensity View tab shows intensity data for the selected ROI shape as a table of values Figure 3 10 6 3 2 1 aaa Molol Manager Linapeceor Retuita Gripe Pane baberctiey Wia si g1 1 l 7 i 4 5 a a7 E T miro 271 0 307 0 140 281 0 54 0 240 0 263 0 297 0 165 0 en ides zii 301 0 166 0 478 0 244 0 282 0 113 0 176 0 4510 Max 1706 00 253 0 313 0 377 0 433 0 528 0 46 0 7b0 0 479 0 4550 607 0 Mean S76 28 272 0 316 0 167 0 406 0 588 0 Fo7 0 786 0 379 0 427 0 524 0 671 0 T l o Eos ame Tl ee Peri ae Ready Figure 3 10 6 3 2 1 Intensity view of pixel intensities The Intensity View window shows intensity values for a selected channel The selected channel can be changed using the menu towards the top right of the window It also shows summary intensity data to the right of the tabular display of intensities including Minimum intensity value Maximum intensity value Mean intensity value Sum of all intensity values Standard deviation X and Y co ordinates of the ROI shape Width and height of the ROI and X and Y co ordinates of the centre of the ROI shape If the ROI shape is moved or resized or another ROI shape is chosen the values will be automatically updated in the Intensity View wind
33. ct or dataset to be removed 2 Inthe Edit menu select Remove or Remove from current project for a dataset This removes the selected project or dataset Orphaned Datasets will be created to hold the removed dataset s 3 The removed projects or datasets will go to Orphaned Datasets which appears on top of the tree view The number in the bracket shows how many removed datasets are in When you remove a project the dataset s in it will be listed in the Orphaned Datasets and therefore you will not see the name of the project but only the dataset s A project or dataset is only removed from a project it is not deleted from the system Copyright 2006 2007 University of Dundee All Rights reserved Page 30 OMERO clients User Guide 3 3 4 Expanding a project to see constituent datasets In the left hand pane you might see projects listed but not their datasets Figure 3 3 4 1 The number in square brackets after the project name is the number of datasets belonging to the project To see all datasets belonging to a project click the Expand icon All datasets associated with the selected project will now be shown Figure 3 3 4 2 This icon will change appearance to to show that the project has been expanded to show datasets clicking the icon again will collapse the display to show just the project again Note that in Figure 3 3 4 1 the AnotherDemoProject image has no datasets so cannot be expanded
34. d Page 102 OMERO clients User Guide 3 10 5 3 1 Moving a single ROI shape To adjust the position of an ROI shape 1 Select the Selection toolbar button y 2 Inthe Image Viewer window move the mouse pointer to a point inside the ROI shape you wish to move 3 Hold down the mouse button the mouse pointer will change to the drag cursor 4 Drag the shape to the desired location 5 Release the mouse button Copyright 2006 2007 University of Dundee All Rights reserved Page 103 OMERO clients User Guide 3 10 5 3 2 Resizing a single ROI shape To adjust the shape of an ROI shape 1 Select the Selection toolbar button w 2 Inthe Image Viewer window move the mouse pointer to the border of the ROI shape you wish to move Hold down the mouse button the mouse pointer will change to the resize cursor Adjust the ROI shape to the desired appearance Release the mouse button or p For ROI shapes propagated across multiple z sections or timepoints resizing an ROI shape will only change the shape on the one plane not all z sections or timepoints Copyright 2006 2007 University of Dundee All Rights reserved Page 104 OMERO clients User Guide 3 10 5 4 Changing the appearance of an ROI shape Various changes to the visual display of a selected ROI shape can be made through the ROI Shape Inspector see Figure 3 10 5 4 1 Measurement Toul DMOHeqh_ O01 dy Controls Options ana Pooja mh
35. de 3 1 Getting to know the Data Manager Every time you log in OMERO insight you will see Data Manager s default screen which consists of several areas of interest as labelled in Figure 3 1 1 1 The left hand pane shows projects and datasets category groups categories or images in a hierarchical manner Note that on first accessing OMERO insight this pane will be empty until you create a project 2 The right hand pane shows information relating to the currently selected project dataset category group category or image and will be blank if none exists or none is selected 3 Above the two panes are three distinct navigational areas From the top of the page these are a Application wide toolbar This gives access to options that remain constant throughout use of the Data Manager b The Projects Categories and Images tabs These specify what information is shown in the left hand pane c Context specific toolbar This provides options specific to whether Projects and Datasets Category Groups and Categories or Images are being shown in the left hand pane 4 Finally there are five application menus each offering options based on the current status of OMERO insight The menus available are File Edit View Window and Help Copyright 2006 2007 University of Dundee All Rights reserved Page 21 OMERO clients User Guide 000 Jean Marie Burel s Data Manager File Edit View Window Help EAL S a T a
36. de wheel if your operating system supports this Nlsers dave Deskiog fome Test images img AID d Fo i Poom Window as YO E ae 231 2 231 We S0H 50 x20 ab 2 2 3 T 0 0 Figure 3 9 3 2 1 Image Viewer and Zoom window Copyright 2006 2007 University of Dundee All Rights reserved Page 71 OMERO clients User Guide 3 9 3 3 Scale bar The Image Viewer by default includes a scale bar in the bottom right corner of the image In Figure 3 9 3 1 1 the scale bar shows a length of 5 nanometres the default setting You can configure how the scale bar is displayed using the View menu To remove the scale bar from the current image display 1 Select the View menu 2 Select the Show Scale bar option To show the scale bar repeat the steps above To change the length of the scale bar Select the View menu 1 2 Select Scale bar length in nanometres 3 Then e Either choose a length from the options available e Or choose Custom and in the pop up window that appears enter your preferred length in the Value field and press Enter 4 The scale bar length and label will now be adjusted To change the colour of the scale bar Select the View menu Select Scale bar colour option Choose from one of the colour options available The scale bar colour will now be adjusted The scale bar will not appear if there is not enough space ee Copyright 2006 2007 University of Dundee All Rights reserved Page 72 O
37. e 2 2 1 Log in screens for OMERO importer and OMERO insight Once logged in successfully the appropriate OMERO application will open up Copyright 2006 2007 University of Dundee All Rights reserved Page 4 OMERO clients User Guide 2 3 Importing images OMERO currently allows you to import the following file formats Bio Rad PIC pic Excluding e multi plane stitched files e annotated ROI images Bitmap bmp Excluding e Compressed images e Mutli plane Color images Deltavision dv r3d r3d_d3d Digital Imaging and Communications in Medicine dcm dicom dic Excluding e Compressed images Graphics Interchange Format gif Imaris Raw Images ims 5 0 format and 5 5 format Improvision Tiff tif Joint Photographic Experts Group jpeg jpg Excluding e JPEG2000 images Leica lei Format lei Leica Image Format lif Metamorph STK stk Openlab Raw raw Openlab LIFF liff Portable Gray Map pgm Portable Network Graphic png Tagged Image File Format tif tiff Visitech XYS xys Zeiss Laser Scanning Microscopy lsm Copyright 2006 2007 University of Dundee All Rights reserved Page 5 OMERO clients User Guide This is a very open standard so expect a few variant types to be unsupported We do however do extensive tiff testing so the format is generally well supported The Visitech importer does not fully support all Visit
38. e image 3 7 4 2 Categorising multiple images 3 7 4 3 Viewing images in a category 3 7 4 4 Removing an image from a category 3 8 Sorting and finding images 3 8 1 Sorting images 3 8 2 Retrieving selected images 3 8 3 Finding images with Find in Tree 3 9 Viewing images 3 9 1 Viewing a specific Channel 3 9 2 Additional viewing options 3 9 2 1 Colour and greyscale viewing 3 9 2 2 Movie viewing across channels 3 9 2 3 Channel configuration 3 9 2 4 Image information 3 9 2 5 Annotation View 3 9 3 Magnification 3 9 3 1 Magnifying the whole image 3 9 3 2 Magnifying an area of the image 3 9 3 3 Scale bar Copyright 2006 2007 University of Dundee All Rights reserved Page 18 OMERO clients User Guide 3 9 4 Viewing z sections and timepoints 3 9 4 1 Automated viewing of z sections and timepoints 3 9 4 2 Selecting z section and timepoints 3 9 4 3 Additional Movie Player options for z section and timepoint viewing 3 9 5 lmage Rendering options 3 10 Introduction to the Measurement Tool 3 10 1 Accessing the Measurement Tool 3 10 2 The Measurement Tool interface 3 10 3 Creating ROIs 3 10 3 1 What is an ROI 3 10 3 2 Creating a single shape 3 10 3 3 Adding multiple ROI shapes on one plane 3 10 3 4 Creating an ROI across z sections and timepoints 3 10 4 Saving and loading ROIs 3 10 4 1 Saving ROIs 3 10 4 2 Loading ROIs 3 10 5 Editing ROIs 3 10 5 1 Selecting ROIs 3 10 5 2 Annotation and labelling 3 10 5 2 1 Annotating an existi
39. e the currently displayed data e Select the Save button e Specify the location of the file to be saved e Choose the format for the saved data At present this is limited to Comma Separated Variable CSV format e Select Save Copyright 2006 2007 University of Dundee All Rights reserved Page 117 OMERO clients User Guide 3 10 6 3 Viewing pixel intensity values Pixel intensity values for an individual ROI shape can be viewed graphically or as figures in tabular format 3 10 6 3 1 Graphical view 3 10 6 3 1 1 Configuring the Graph view 3 10 6 3 1 2 Saving graphical views 3 10 6 3 2 Intensity View Copyright 2006 2007 University of Dundee All Rights reserved Page 118 OMERO clients User Guide 3 10 6 3 1 Graphical view Selecting the Graph Pane tab shows intensity values as a histogram Additionally a line profile will be shown for line ROI shapes see Figure 3 10 6 3 1 1 O O Measurement Tool Users dave Desktop usable image Test Images Img_R3D dv_ anas Molol im ela 7 1 a Manager L Inspector E Results H Graph Pane Intensity View Line Profile 5 10 15 20 235 30 A 2 45 50 55 BO 65 FO 7S Ue OOS Pixel 457 525 61 Histogram 20 Li ils mT itl it 730 i 1250 1300 Intensity Eas7 E528 n617 Ready Figure 3 10 6 3 1 1 Graph pane view of pixel intensities If the ROI shape is moved or resized or another ROI shape is chosen
40. ech metadata included in the accompanying html file Since the following formats bmp gif jpeg pgm png tiff do not contain metadata the importer will use default values for the pixel size and channel meta data You can use OMERO importer to select images from a storage disk and import them into the OMERO system OMERD imparte ieee pt Text Debug Test LI Tent imagan E impart Queue Li Carigra Misca i ETHS J iah H LD mirant ES hppa i ommsda T ome ii soi opt one dient 1 Denar Ermana cdi T wa O Papiri i wuart Di Pipiri A dea 2 OPAL Li ia OP hwir 2 MEHET pia Spotty T apa hpl ai ahai muag Li User deur en LD vidios a we vir dock die phe am a Flags Gara EE vi T ing Did E PAWS 2F FP a Te P TIIT Cl POL eo de ei imi r Eer Fumar Al supported file byari E Z CASED HI sete eee ery g Figure 2 3 1 OMERO importer in File Viewer mode Copyright 2006 2007 University of Dundee All Rights reserved Pegan irpo Page 6 OMERO clients User Guide a 1 Sa i mport Import these images inte which dataset Project Select Project 4 Ada Dataset Empty Set i Add File Naming The imported file name on the server should include C the full path and file name from you local system a partial path which includes the file name and 1 ofthe directories mmedciately before It Archive the original imported file s to the
41. een rigorously tested to ensure it works as expected Errors however may occur and a window will appear Figure 4 2 1 inviting you to submit feedback about the error Providing this information is not required but will help the development team identify and overcome the cause of the error Submitting your email address is optional and if you do this information will only be used to contact you for more details about what you were doing when the error occurred Comment Comments Error Message An error message has been generated by the application T help us improve our software please fill aut the following form Your personal details are purely optional and will only be used for development purposes Pease note that your application may need to be restarted to work properly o E i OO Opiom Errail What you were doing when you crashed E Cancel J Send Figure 4 2 1 Error feedback form Copyright 2006 2007 University of Dundee All Rights reserved Page 140 OMERO clients User Guide 5 Background information This User Guide concentrates on providing a practical guide to managing viewing and manipulating image in OMERO but the following information in this section gives a brief outline of the principles and concepts used by OMERO 5 1 What is OMERO 5 2 The OMERO Environment client and server 5 3 5 Dimensional images 5 4 The OMERO Data Model and Hierarchies Copyright 2006 2007 University of Dundee A
42. el Figure 3 8 2 1 Filter images retrieval window Clicking the Images tab see Section 3 3 2 results in a new window being displayed the Filter Images Retrieval window Figure 3 8 2 1 This allows you to specify which image filenames you would like to see listed in the left hand pane You have three choices 1 Select images from chosen datasets 2 Select images from chosen categories 3 Select all images in your collections Select the Image menu button to see the Image menu shown in Figure 3 8 2 2 This allows you to specify how Filter Images Retrieval will work On choosing either of the first two options in the list above the Filter Images Retrieval allows you to select those datasets or categories from which you wish to retrieve images All image filenames found will then appear in the left hand pane Copyright 2006 2007 University of Dundee All Rights reserved Page 54 OMERO clients User Guide eee LESADA Test Images 2 erp bd eeu sik Test Images 23ep dksunsk Plmages in Categories Test Images 654 Abemp stk All ery Images Test images 654 Anemp sik si Test images a A PDE a aj aj aj aj Find a Firg hee h Pied Presitus Figure 3 8 2 2 Menu for configuring Filter Images Retrieval Copyright 2006 2007 University of Dundee All Rights reserved Page 55 OMERO clients User Guide 3 8 3 Finding images with Find in Tree The Find in Tree feature works in a similar
43. electing the Renderer option This brings up the Display Settings window shown in Figure 3 9 5 1 8 A Display Settings 041206_3HT3_stain go1_3HT3 Controls tp Mapping Device Settings D a pije i _ Immediate Update Miri Max 2484 Start 124 End 1894 Show Advanced Options Save Undo All Figure 3 9 5 1 Display Settings Adjusting the rendering parameters will result in an immediate visual change to the image shown in the Image Viewer except when adjusting the values of the horizontal slider By default the image shown in the Image Viewer will be updated when the knobs of the horizontal slider are released For an immediate update check the Immediate Update check box Copyright 2006 2007 University of Dundee All Rights reserved Page 78 OMERO clients User Guide The horizontal slider allows you to specify start and end values for the interval of the raw data you wish to map This is specified separately for each channel Alternatively you can manually enter values in the Start and End fields Currently you can only select values between the displayed Min and Max values 0 and 2484 in Figure 3 9 5 1 The vertical slider allows you to specify a range of the colour space i e a sub interval of 0 255 This allows you to increase or decrease the overall brightness of the image Copyright 2006 2007 University of Dundee All Rights reserved Page 79 OMERO clients Use
44. ems Copyright 2006 2007 University of Dundee All Rights reserved Page 40 OMERO clients User Guide ry ey oy Save annotation Do you want to apply this annotation only to tubhiswt 40 tubhiswt C2 _TP20 tiff or to j all items in the annotation list Figure 3 6 3 2 Multiple annotation confirmation Copyright 2006 2007 University of Dundee All Rights reserved Page 41 OMERO clients User Guide 3 7 Categorising images OMERO insight allows you to create categories for use in managing your images as a separate means of organisation from the Project Dataset structure To do this first you create a category group and then create one or more categories within the category group Once you have some Categories you can then use these to categorise your images Icons used gf denotes a category group e denotes a category Bi denotes a categorised image Eal denotes a categorised image that also has one or more annotations 3 7 1 Creating category groups 3 7 2 Creating categories 3 7 3 Removing categories and category groups 3 7 4 Categorising images 3 7 4 1 Categorising a single image 3 7 4 2 Categorising multiple images 3 7 4 3 Viewing images in a category 3 7 4 4 Removing an image from a category Copyright 2006 2007 University of Dundee All Rights reserved Page 42 OMERO clients User Guide 3 7 1 Creating category groups Creating a category group is a similar process to creating a P
45. ent state of the image alternative state is BE enable toggling between colour model and greyscale display e To switch from colour display to greyscale select Ei e To switch from greyscale to colour display select a The above options can also be chosen by opening the Controls menu and selecting the Models option This allows you to choose between Colour and Greyscale options Copyright 2006 2007 University of Dundee All Rights reserved Page 62 OMERO clients User Guide 3 9 2 2 Movie viewing across channels gt alternative state is il enable viewing single channel views of the image as a movie 1 To start the movie select This will display the image for a short period using each of the currently selected channels in turn 2 The movie runs on a loop and will continue until you stop it To stop the movie select il The image then reverts to its appearance before the movie started This option is available for the Image Viewer s Standard View and Annotation View modes Movie options for viewing z sections and timepoints are described in Section 3 9 4 Copyright 2006 2007 University of Dundee All Rights reserved Page 63 OMERO clients User Guide 3 9 2 3 Channel configuration P The Colour Picker button allows you to configure the channel corresponding to a specific channel button To associate a specific channel with a channel button Click on the Colour Picker button In the menu that appe
46. h for a specific image s 3 8 1 Sorting images 3 8 2 Retrieving selected images 3 8 3 Finding images with Find in Tree Copyright 2006 2007 University of Dundee All Rights reserved Page 51 OMERO clients User Guide 3 8 1 Sorting images A number of options are available for sorting a collection of images These are provided in the context specific toolbar labelled as 3c in Figure 3 1 1 directly below the Projects Categories and Images tabs Figure 3 8 1 1 and are available to a list of images Figure 3 8 1 1 Toolbar providing sort options These options are 13 Alphabetical sort Select this option to sort image file names in alphabetical order In the illustration in Figure 3 8 1 1 this option is selected and hence the icon appears shaded a Date sort Select this option to sort image file names in order of the date they were taken on the microscope and if this information is not available in order of the date of import into OMERO If the list of images shows more than one open dataset or category images are sorted alphabetically or by date only within their parent dataset or category although the order in which datasets or categories appear may change ae This option allows you to toggle between showing a truncated path name and full path name for each listed image Figure 3 8 1 2 and Figure 3 8 1 3 show the difference in image display names 5 Grop 2 2 T Grup 7 1 T DemoCa
47. h the Measurement Tool see Figure 3 10 1 Copyright 2006 2007 University of Dundee All Rights reserved Page 84 OMERO clients User Guide 3 10 2 The Measurement Tool interface It is worth familiarising yourself with the Measurement Tool user interface shown in Figure 3 10 1 It consists of two key areas a series of buttons identified by icons and below that a series of tabbed navigation options Additionally there are menu options available at the top of the application window and in specific situations available by right clicking the mouse The Measurement Tool has a toolbar giving access to the key features of the tool shown in Figure 2 Figure 3 10 2 1 4 SI PROOlO N N te G al Figure 3 10 2 1 Measurement Tool toolbar Below this are a series of tabs giving access to key views of data relating to ROIs present in the selected image see Figure 3 10 2 2 4 Manager J Inspector A Results HH Graph Pane El Intensity View Figure 3 10 2 2 Measurement Tool s tab navigation In turn these tabs give access to the following features of the Measurement Tool e Manager shows a hierarchical view of all ROIs and constituent shapes present in the image This allows you to select an individual ROI shape or ROI a collection of shapes for analysis or editing e Inspector allows you to edit the appearance of an individual ROI shape including colour of line fill and any text ass
48. he window that appears see Figure 3 3 1 1 enter the name of the new project You can optionally add a textual description of the project Select Save to confirm Your project should now be created Figure 3 3 1 2 shows a new project created and named DemoProject Project Add a mew project Name Description Figure 3 3 1 1 Insight s Add a new project window Copyright 2006 2007 University of Dundee All Rights reserved Page 25 OMERO clients User Guide Figure 3 3 1 2 Data Manager showing details of a selected project To create a dataset in OMERO insight 1 Select the project in which you want to create the dataset The right hand pane now shows information about the selected project see Figure 3 3 1 3 From the File menu select Add New Dataset Or select the icon 3 In the window that appears enter the name of the new dataset and a textual description if you wish 4 Select Save to confirm the addition 5 The dataset should now be listed in the left hand pane under the relevant project see Figure 3 3 1 4 Copyright 2006 2007 University of Dundee All Rights reserved Page 26 OMERO clients User Guide Ae0b Jean Marie Burel s Data Manager File Edit View Window Help D SQ ESL a e Projects t Categories Lf gt Y Jean Marie Burel gt Orphaned Datasets A A A gt Bi Elite Project 1 Create new element Dataset gt a f rt 1 me
49. icking on an icon will bring up the corresponding tab in the Working area see Section 3 10 2 5 Copyright 2006 2007 University of Dundee All Rights reserved Page 133 OMERO clients User Guide 3 11 2 5 Additional image information the Working Area The Working Area is an area at the bottom of the Hierarchy Viewer window where detailed information about the currently selected image is available Any image with a thumbnail shown in the Hierarchy Viewer can be selected by single clicking or double clicking the image To show the Working Area Figure 3 10 2 5 1 1 Select the Working Area toolbar button to show the Working Area when the Working Area is visible select this button again to hide it 2 Use your mouse to drag the Working Area to the desired size Jee BE S South Amarica brani gt main bh CI TPL ely 28 20ST ns South Ararical me pardi faa Codoes bead 1 EEEEE HEB EY F et eT a P FN DORE EEE z z z z n z BODO Baas 2 z T amn F Egan thew bie a Toia Lamesi d Figure 3 10 2 5 1 Hierarchy Viewer showing Working Area The Working Area illustrated in Figure 3 10 2 5 1 provides similar information to the right hand panel of the Data Manager There are five tabs each providing access to a specific Working Area feature and each described below 1 Annotation Selecting this tab views all current annotations for the selected image You Copyright 2006 2007 University of D
50. idth menu and selecting the appropriate value e Change the colour of the ROI shape s text the ROI shape s fill for polygonal ROI shapes the ROI shape s boundary line the ROI shape s measurement text To change a colour Double click the appropriate coloured area in the Inspector window 2 Inthe colour picker window that appears select the appropriate colour from the options displayed 3 Adjustments can be made to the Alpha value by using the slider 4 Select Accept to make the change Copyright 2006 2007 University of Dundee All Rights reserved Page 107 OMERO clients User Guide 3 10 5 4 3 Hiding ROI shapes To hide selected ROI shapes from display 1 Open the ROI Manager see Figure 3 10 5 1 1 2 For the ROI shapes to be hidden uncheck the Visible checkbox Repeating the above actions will make currently hidden ROI shapes visible again Copyright 2006 2007 University of Dundee All Rights reserved Page 108 OMERO clients User Guide 3 10 5 5 Deleting a single ROI shape To delete an individual ROI shape 1 Select the shape to be deleted by clicking on the shape in the Image Viewer window for rectangles ellipses and polygons clicking inside the shape will select it 2 Then e Either press the Delete key on your keyboard to delete the selected shape e Or open the ROI Manager right click on the selected ROI shape select ROI Management Options and then Delete Copyright
51. image in the Image Viewer 2 ROls associated with the image will be automatically loaded so long as they were created on the same computer used to view them Copyright 2006 2007 University of Dundee All Rights reserved Page 96 OMERO clients User Guide 3 10 5 Editing ROIs 3 10 5 1 Selecting ROIs 3 10 5 2 Annotation and labelling 3 10 5 2 1 Annotating an existing ROI shape 3 10 5 2 2 Labelling Images 3 10 5 3 Moving or resizing a single ROI 3 10 5 3 1 Moving a single ROI shape 3 10 5 3 2 Resizing a single ROI shape 3 10 5 4 Changing the appearance of an ROI shape 3 10 5 4 1 Adjusting display of annotation text 3 10 5 4 2 Adjusting display of the ROI shape 3 10 5 4 3 Hiding ROI shapes 3 10 5 5 Deleting a single ROI shape 3 10 5 6 Editing multiple ROI shapes and ROIs Copyright 2006 2007 University of Dundee All Rights reserved Page 97 OMERO clients User Guide 3 10 5 1 Selecting ROIs There are a number of ways to select one or more ROI shapes for editing Using the Image Viewer window e To select a single ROI shape on a single plane click on the ROI shape in the Image Viewer window e To select multiple ROI shapes on a single plane right click on one ROI shapes and select Select All from the menu that appears e To select only ROI shapes of the same type right click on one ROI shapes and select Select Same from the menu that appears Using the ROI Manager e Open the Manager view see Figure 3 10 5 1 1
52. l by setting the magnification of the image or by using the lens feature This feature works for all three Image Viewer modes Standard View Annotation View and Split View 3 9 3 1 Magnifying the whole image 3 9 3 2 Magnifying an area of the image 3 9 3 3 Scale bar Copyright 2006 2007 University of Dundee All Rights reserved Page 68 OMERO clients User Guide 3 9 3 1 Magnifying the whole image To magnify the whole image use the Zoom feature 1 2 3 Open the Zoom menu Choose from one of the predefined magnification levels The display of the Image Viewer will change to show the selected image Figure 3 9 3 1 1 This works in a similar fashion in Standard View Annotation View and Split View modes For increased magnification you may need to use the Image Viewer s scroll bars to view all parts of the image to avoid this you can resize the Image Viewer window to show an increased area of the image Urersidave Desktop ome Tesi Imagesiimg AtDde T aie E j Eang oOo a A i jg Z 2 3 T 0 0 Figure 3 9 3 1 1 Image Viewer showing magnified image Copyright 2006 2007 University of Dundee All Rights reserved Page 69 OMERO clients User Guide 3 9 3 2 Magnifying an area of the image The Lens feature allows you to see an area of the image at a greater magnification level than the Zoom feature It also allows you to see the magnified section alongside the image as a whole It w
53. ll Rights reserved Page 141 OMERO clients User Guide 5 1 What is OMERO OMERO is a set of software tools that supports image data management visualisation and annotation OMERO tools include e an OMERO Server e and a series of client applications e OMERO webadmin e OMERO importer e OMERO insight Copyright 2006 2007 University of Dundee All Rights reserved Page 142 OMERO clients User Guide 5 2 The OMERO Environment client and server OMERO s design follows a standard client server architecture A single installation of an OMERO server will usually be used for an entire laboratory or imaging facility Image data and metadata are typically stored on a central computer running the OMERO server and then accessed via a standard Ethernet network using OMERO client applications that run on a user s workstation or laptop computer The OMERO Server manages all image metadata date size channel names etc but also contains an image rendering facility that generates fully rendered images ready for display in an OMERO client application Copyright 2006 2007 University of Dundee All Rights reserved Page 143 OMERO clients User Guide 5 3 5 Dimensional images OMERO allows handling of up to 5 dimensional images As well as the conventional x and y dimensions you may store view and manipulate z sections channels and timepoints The relationship of these multiple dimensions is illustrated in Figure 5 3 1
54. mages among group users Assuming the appropriate permissions have been granted by the image owner it will be possible for e You to select another user and view their images e Other people with an OMERO account to view your images for which you have enabled permission for others to view To select another user view and if desired annotate their images e Click on the Switch user icon Eey Or open the File menu and select Switch user e Choose the OMERO group in which the user belongs e Select the user from the menu that appears see Figure 3 4 1 and select Apply The user s data will appear in a new Data Manager window Switth Weer Swatch user F a Select a user and vlew his her data jet a Groups _Swedbow Lab OMERO F Users 4 Jean Marie Burel ad Brian Loranger 64 Carriona MacCaulay 63 Donald MacDonald a jason Swedigw Cancel Figure 2 4 1 Switch User selection menu Copyright 2006 2007 University of Dundee All Rights reserved Page 34 OMERO clients User Guide Copyright 2006 2007 University of Dundee All Rights reserved Page 35 OMERO clients User Guide 3 5 Additional information about projects datasets and images You can view additional information to a selected project dataset or image This is available in the right hand pane of the Data Manager e The Properties tab shows you the name and description of the selected project dataset or image In future versions of OMERO insight
55. ng ROI shape 3 10 5 2 2 Labelling Images 3 10 5 3 Moving or resizing a single ROI 3 10 5 3 1 Moving a single ROI shape 3 10 5 3 2 Resizing a single ROI shape 3 10 5 4 Changing the appearance of an ROI shape 3 10 5 4 1 Adjusting display of annotation text 3 10 5 4 2 Adjusting display of the ROI shape 3 10 5 4 3 Hiding ROI shapes 3 10 5 5 Deleting a single ROI shape 3 10 5 6 Editing multiple ROI shapes and ROIs 3 10 6 Viewing ROI information 3 10 6 1 Viewing summary ROI information 3 10 6 2 Measurement results 3 10 6 2 1 Showing summary results 3 10 6 2 2 Refreshing summary data 3 10 6 2 3 Saving summary data 3 10 6 3 Viewing pixel intensity values 3 10 6 3 1 Graphical view 3 10 6 3 1 1 Configuring the Graph view 3 10 6 3 1 2 Saving graphical views 3 10 6 3 2 Intensity View 1 The Hierarchy Viewer viewing multiple images 1 1 Viewing an image from the Hierarchy Viewer 1 2 Using the Hierarchy Viewer 11 2 1 Adjusting thumbnail display 3 3 3 3 Copyright 2006 2007 University of Dundee All Rights reserved Page 19 OMERO clients User Guide 1 2 2 Display Tree View of images 1 2 3 Sorting images 1 2 4 Managing images in the Hierarchy Viewer 1 2 5 Additional image information the Working Area 2 Managing windows in OMERO insight 3 Closing OMERO insight _ et b b 1 i 3 3 3 3 3 3 Copyright 2006 2007 University of Dundee All Rights reserved Page 20 OMERO clients User Gui
56. ng images in a category 3 7 4 4 Removing an image from a category Copyright 2006 2007 University of Dundee All Rights reserved Page 46 OMERO clients User Guide 3 7 4 1 Categorising a single image To categorise an individual image 1 Select the image filename 2 Then e Either in the Edit menu select Categorise e Or select the toolbar button and then Categorise from the pop up menu that appears 3 Inthe right hand pane you will initially see a list of available category groups Select the appropriate category group and expand it by selecting the Expand button p 4 Tick all categories you wish to add the selected image to Select All and Deselect All buttons are available to speed up the task of selection 5 Select Save to confirm the categorisation Copyright 2006 2007 University of Dundee All Rights reserved Page 47 OMERO clients User Guide 3 7 4 2 Categorising multiple images If you wish to add more than one image to the same category or categories the steps described in Section 3 7 4 1 can be applied for multiple selected images Copyright 2006 2007 University of Dundee All Rights reserved Page 48 OMERO clients User Guide 3 7 4 3 Viewing images in a category To view all images in a selected category 1 Select the Categories tab 2 Inthe left hand pane expand the category group and select your chosen category 3 The list will expand to show all images currently in that catego
57. niversity of Dundee All Rights reserved Page 14 OMERO clients User Guide 2 4 2 Viewing a selection of images the Hierarchy Viewer A selection of images for viewing can be made at different levels based on how your data is organised in OMERO You can e Select one or more projects this selects all images in each dataset belonging to the selected project s groups e Select one or more datasets this selects all images in the selected datasets e Select one or more images by using the keyboard and or mouse to select more than one image filename from the list shown in the left hand pane You can also select images according to the Category they belong to which is another way of organising your data you define your own category groups and categories and then you can place your images into one or more categories For more on categories see Section 3 7 To view a selection of images 1 Inthe Data Manager select the first project dataset category group category or image you wish to view by clicking once to highlight it 2 Use the appropriate keys for your operating system to select subsequent projects datasets category groups categories or images You can only select multiple objects of the same level for example you can select 5 images but not one dataset plus 5 images However you can select individual datasets from different projects if desired 3 Once you have your selection select the Browse butt
58. ociated with the image e Results view shows a summary of key measurement data for all ROI shapes present It allows you to select an individual ROI shape for further detailed analysis e Graph Pane generates graphical representations histogram and for line ROI shapes line plots of intensity values by channel for the selected ROI shape These can be saved as images e Intensity View provides numerical data of individual pixel intensity values plus values such as mean maximum and minimum values plus an option to export this data for viewing in spreadsheet applications such as Excel as a CSV file Copyright 2006 2007 University of Dundee All Rights reserved Page 85 OMERO clients User Guide 3 10 3 Creating ROIs You can create Regions of Interest ROIs of varying types on a single plane which can then be expanded to become multi dimensional 3 10 3 1 What is an ROI 3 10 3 2 Creating a single shape 3 10 3 3 Adding multiple ROI shapes on one plane 3 10 3 4 Creating an ROI across z sections and timepoints Copyright 2006 2007 University of Dundee All Rights reserved Page 86 OMERO clients User Guide 3 10 3 1 What is an ROI In OMERO we use the following definitions e ROI a multi dimensional object consisting of one or more ROI shapes indicated by the icon e ROI shape a two dimensional object that appears on one plane only indicated by the icon 7 An ROI shape also automatically exists as an RO
59. of annotation text cseseeeees 106 3 10 5 4 2 Adjusting display of the ROI shape ssseeeee 107 3 10 5 4 3 Hiding ROI SHADES vices scssicnetscicisssicccnssandssarenabanenanswaaans 108 Copyright 2006 2007 University of Dundee All Rights reserved OMERO clients User Guide 3 10 5 5 Deleting a single ROI Shape secccceeesseeeeeeeeeenseeeeeees 109 3 10 5 6 Editing multiple ROI shapes and ROIS eeeeeeeeeees 110 3 10 6 Viewing ROI informatiOn cccccesssseeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeees 111 3 10 6 1 Viewing summary ROI information cccsssseeeeeeeseeeeeees 112 3 10 6 2 Measurement reSults c sseeeeeeeeeeeseeeeeeeeeeeeesneeeeeeeeeensseeneees 113 3 10 6 2 1 Showing summary results ccccesesseeeeeeeeeeeeeeeeeeeeeees 114 3 10 6 2 2 Refreshing summary Cata ccccsessseeeereeeeeeeeseeeeeeeees 116 3 10 6 2 3 Saving summary data esseseeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeees 117 3 10 6 3 Viewing pixel intensity values sseeeeeeeeeeeeeeeeeeeeeeeeeeees 118 3 10 6 3 1 Graphical VIEW sisisicseacecndsssainsranctenciestinenasaniieicestorenasdianaies 119 3 10 6 3 1 1 Configuring the Graph View csseeeeeeeeeeeeeeeees 120 3 10 6 3 1 2 Saving graphical ViOWS ccceesseseeeeeeeeeeeeeeeeees 121 3 10 6 3 2 Intensity VIEW ciaseinrsinipienirssiaanies ai siniendeneetnairiaetundansinns 122 3 11 The Hierarchy
60. on Fil This brings up a Hierarchy Viewer window showing a series of thumbnails one for each image in your selection see Figure 2 4 2 1 Copyright 2006 2007 University of Dundee All Rights reserved Page 15 OMERO clients User Guide an iban Parar HITI Larss Fide Ddin vie Wiara Help J HITI minia e badi HEHA gt iL HTI a Boe ATE OL OS ede Gan G T me RA eis WUKODOR lo eleleiis pangooon r P JE r lelel lsisiel gt F r oon Dome e G epr e ieia Figure 2 4 2 1 Hierarchy Viewer showing simple selection of images The Hierarchy Viewer also provides e a range of tools for viewing individual thumbnails e options to rearrange the display of thumbnails e facilities to display and edit information relating to a particular thumbnail See Section 3 10 2 for more details Copyright 2006 2007 University of Dundee All Rights reserved Page 16 OMERO clients User Guide 2 5 Saving images You can save a copy of any image displayed in the Image Viewer in a number of different image formats This may be particularly useful for having a copy to include in a presentation or publication 1 Open the Controls menu and select the Save As option Or select the Al icon in the Image Viewer 2 Inthe Save Image window you can a Specify the name of the saved image file b Select the destination of the saved image file this can be set to be the default folder for future save operations c
61. orks in a similar fashion in Standard View Annotation View and Split view 1 Open the Zoom window e Either select the Lens toolbar button A e Oropen the Controls menu and select the Lens option 2 The Zoom window will now appear beside the Image Viewer window and shows a magnified area of the image Below the image is additional information on the dimensions of the magnified image The area of the magnified image is outlined in the main Image Viewer window Figure 2 9 3 2 1 To redefine the area of the image being magnified 1 Click the mouse pointer on the highlighted area in the main Image Viewer 2 Drag the highlighted area to the area of the image you wish to see magnified 3 The Zoom window will be updated to reflect the change in area To change the size of the magnified area 1 Inthe Zoom window select the Lens menu 2 Choose from one of the predefined window sizes You may need to scroll or resize the Zoom Window to see all of the magnified area To change the magnification level 1 Inthe Zoom window select the Zoom menu 2 Choose from the predefined list of magnification options 3 The dimensions shown will be updated to reflect your choice To change the units of the dimensions shown in the Zoom Window select the Units menu and choose between microns and pixels You can also zoom using the mouse Copyright 2006 2007 University of Dundee All Rights reserved Page 70 OMERO clients User Gui
62. otation will appear within the ROI shape 3 Use the ROI Inspector i Select the shape to be annotated the selected ROI shape will be highlighted ii Open the ROI Inspector iii Double click on the Annotation field iv Edit the existing text or add new texts See details of adjustments that can be made to the appearance of the annotation text in Section 3 10 5 4 1 Copyright 2006 2007 University of Dundee All Rights reserved Page 100 OMERO clients User Guide 3 10 5 2 2 Labelling Images To add a text label ROI shape Select the Text toolbar button a Click on the area of the image in which the label is to be added A text box with the word text will appear Double click on the text box to add the desired label text The label is now shown resizing the area of the text label will adjust the size of the text Be Note that the text label will exist as an ROI with a single shape and appear as such in the ROI Manager Inspector and Results views Double clicking on the text ROI in the ROI Manager and Inspector allows you to edit the text Copyright 2006 2007 University of Dundee All Rights reserved Page 101 OMERO clients User Guide 3 10 5 3 Moving or resizing a single ROI Once an ROI shape has been created it is possible to move or resize it as required 3 10 5 3 1 Moving a single ROI shape 3 10 5 3 2 Resizing a single ROI shape Copyright 2006 2007 University of Dundee All Rights reserve
63. ough the following options 1 Double click on the image s thumbnail 2 Select the image thumbnail and then select View from the Edit menu 3 Right click on the image thumbnail to display the Edit menu as for option 2 The Image Viewer will then display the image as shown in Figure 2 4 1 Copyright 2006 2007 University of Dundee All Rights reserved Page 126 OMERO clients User Guide 3 11 2 Using the Hierarchy Viewer The Hierarchy Viewer has many additional features to allow access to information about the current image selection 3 11 2 1 Adjusting thumbnail display 3 11 2 2 Display Tree View of images 3 11 2 3 Sorting images 3 11 2 4 Managing images in the Hierarchy Viewer 3 11 2 5 Additional image information the Working Area Copyright 2006 2007 University of Dundee All Rights reserved Page 127 OMERO clients User Guide 3 11 2 1 Adjusting thumbnail display You can adjust the way the sets of thumbnails are displayed in the Hierarchy Viewer in a number of ways Moving a container Select the container and drag it with the mouse to wherever you wish within the Hierarchy Viewer window Resizing a container Click a corner of the container and drag the mouse to resize the container You cannot resize an image by dragging it nor drag an image from one container to another Magnifying an individual thumbnail To enlarge a single thumbnail 1 Select the Magnify button R 2 Move the mouse pointer o
64. out an image displayed in the Image Viewer select the Image Info button The Image details window then appears see Figure 3 9 2 4 1 Image s details image s details Information about the pixels T Size X 512 Size 512 Pixel size X inp 0 314153 Pixel size Y in p 0 314153 Pixel size Z in p 1 0 Close Figure 2 9 2 4 1 Image information window Copyright 2006 2007 University of Dundee All Rights reserved Page 66 OMERO clients User Guide 3 9 2 5 Annotation View One advantage of the Annotation View mode of the Image Viewer is that it allows you to add annotations to an image while looking at it in some detail see Figure 3 9 2 5 1 In this view the Annotations panel is shown in a similar way to the Data Manager showing any existing annotations plus the name of the user who added the annotation and the date they were added like in Data Manager you can add annotations to the image as desired Note that the annotations exist as separate text attributes of the image the image file itself is not annotated me aeration ipt TG Dra ta jil kire AmaE CI hra OO at DOO LF PEGI OT G 1LF IIIF dhith hia daha Tete L arm erinja Dirnt Gb Paty Ta Figure 3 9 2 5 1 Image Viewer Annotation View Copyright 2006 2007 University of Dundee All Rights reserved Page 67 OMERO clients User Guide 3 9 3 Magnification It is possible to view areas of the image in more or less detai
65. ow If the selected ROI shape is part of a multidimensional ROI menus will be provided to allow you to move through each timepoint and or z section In the example shown in Figure 3 10 6 3 2 1 the menu to the left of the figure allows you to change the z section for which the intensity data should be shown Copyright 2006 2007 University of Dundee All Rights reserved Page 122 OMERO clients User Guide Results shown in the Intensity View can be saved in a similar way to the Results view by selecting the Save button at the bottom right of the Intensity View window Copyright 2006 2007 University of Dundee All Rights reserved Page 123 OMERO clients User Guide 3 11 The Hierarchy Viewer viewing multiple images For viewing a selection of images the selection initially appears as a set of thumbnails in a new window the Hierarchy Viewer What you see in the Hierarchy Viewer depends on what you selected Table 3 10 1 summarises how thumbnails are displayed in the Hierarchy Viewer by default using the Hierarchical Layout option Selection JMierarchy Viewer shows O One or more images individually selected All images in a flat view layout see Figure 2 4 1 3 ne dataset or category All images in one container Multiple datasets or categories Multiple thumbnail containers one for each opa TENS hatasetor category oo oo o One project or category group Multiple thumbnail containers one for each ea ae in the project or ca
66. ptions for an example image with 5 z sections numbered 1 2 3 4 5 Play option 2 8 4 5 1 4 5 1 2 3 3 a 2 3 4 5 Loop Backward 4 3 2 1 5 4 3 2 1 Back and forth 2 3 4 5 4 3 2 1 2 Table 3 9 4 3 1 Movie Player Play options To specify which sections or timepoints should be included in the movie 1 Make sure the appropriate option is selected Across Z for z sections only Across T for timepoints only and Across Z and Tto play a movie showing all z sections for each timepoint 2 To specify which individual z section or timepoint is respectively the first and last to be shown in the movie sequence e Either move the left hand slider button to select the first z section or timepoint and the right hand slider button to select the last z section or timepoint e Oruse the Start and End fields to type the number of the first z section or timepoint and last z section or timepoint Copyright 2006 2007 University of Dundee All Rights reserved Page 76 OMERO clients User Guide Copyright 2006 2007 University of Dundee All Rights reserved Page 77 OMERO clients User Guide 3 9 5 Image Rendering options Options are also available to adjust rendering properties Here you adjust how the raw pixels intensity values are mapped to the image displayed on your monitor These are available by e Either selecting the Rendering Options toolbar button Bi e Or opening the Controls menu and s
67. r Guide a Display Settings 041206_3HT3_stain Sgol_3HT3 Controls HMapmng y Device Settings Tempofary Imagi 4 ul Immediate Update Min O Max 2484 Start 124 End 1894 S H ide Advanced Options j Map linear z Gamma Bit Depth I C Noise reduction Save Undo All Figure 3 9 5 2 Display Settings window showing advanced options Advanced image rendering options are available by selecting the Show Advanced Options button Figure 3 9 5 2 This expands the Display Settings window to include options to e Select the mapping curve from a choice of linear polynomial exponential or logarithmic for a channel e For polynomial or exponential curves you can modify the shape of the curve for a channel by adjusting the gamma value e Adjust bit depth e Turn on or off noise reduction Copyright 2006 2007 University of Dundee All Rights reserved Page 80 OMERO clients User Guide Bit depths and values for the vertical slider are the same across all channels the other parameters are specified for each channel The Device Settings tab is not functional in the current version of OMERO insight but will in future versions enable features such as reverse intensity and plane slicing Use the Save button to save rendering settings back to the database for future use Use the Undo All button to reset to the default rendering settings Note that
68. roject 1 2 Select the Categories tab This will bring up a list of existing Category Groups or will be empty if none exist Then e Either click the Create Category Group toolbar button g e Orgo to the File menu and select the New Category Group option In the right hand pane enter the Category Group name and an optional textual description Figure 3 7 1 1 Select Save to confirm Your Category Group should now be listed in the left hand pane Category group Add a mew category group gi Las Name Group Desorption demonstration category group Sive Chase Figure 3 7 1 1 Adding a Category Group Copyright 2006 2007 University of Dundee All Rights reserved Page 43 OMERO clients User Guide 3 7 2 Creating categories Creating a category is a similar process to creating a dataset 1 Select the category group into which the category should go i e make sure it is highlighted in the left hand pane 2 Then e Either click the Create Category toolbar button A e Orgo to the File menu and select the New Category option In the right hand pane enter the Category name and an optional textual description Select Save to confirm Your Category should now be listed in the left hand pane under the appropriate Category Group i oe Figure 3 7 2 1 shows a list of category groups with categories The number in brackets after each category group name indicates how many categories belong to th
69. rsity of Dundee All Rights reserved Page 7 OMERO clients User Guide d Youcan also choose to import a copy of the image file in its original format 5 You can continue to select more images to add to the Import Queue by following steps 2 4 above 6 Once you have finished selecting images select the Import button at the bottom right hand corner of the window The import process will now start You can view the progress in the Status column of the Import Queue window You may also add additional images to the import queue while an import is already running This will only add the images to a new queue when you are ready to import these new images click the import button again to begin importing them 7 When all selected images have status of done your images have been successfully imported and you can then move to OMERO insight to start working with your images OMERO importer has two additional options to File Viewer mode e The Output Text mode clicking on the Output Text tab shows you a brief list of the current import status as files are being imported e The Debug Text mode clicking on the Debug Text tab shows you more technical information about the import status as files are being imported Copyright 2006 2007 University of Dundee All Rights reserved Page 8 OMERO clients User Guide 2 4 Viewing images Once you have imported some images using OMERO importer open OMERO insight to view them either individu
70. ry see Figure 3 7 4 3 1 n Projects E Categories z images E c E T Gj David Sloan H J Orphaned Categories 1 F g 13th December 1 Stavanger 3 af Test images 23srp5dksub stk aF Test Images 654Aremp stk Ef Test Images T2987_G1_BFO1_R3 Figure 3 7 4 3 1 Viewing all images in a selected category Copyright 2006 2007 University of Dundee All Rights reserved Page 49 OMERO clients User Guide 3 7 4 4 Removing an image from a category To de categorise an individual image 1 Select the image filename 2 Then e Either in the Edit menu select Decategorise e Or select the toolbar button and then Decategorise from the pop up menu that appears 3 Inthe right hand pane you will initially see a list of available Category Groups Select the appropriate category group and expand it by selecting the Expand button p 4 Tick all categories from which you wish to remove the selected image Select All and Deselect All buttons are available to speed up the task of selection 5 Select Save to confirm the de categorisation Copyright 2006 2007 University of Dundee All Rights reserved Page 50 OMERO clients User Guide 3 8 Sorting and finding images As you build up collections of images you may wish to sort them into manageable groups or find a specific image or group of images in your collection OMERO insight allows you to sort images by various techniques and also to searc
71. s z sections and timepoints 3 10 4 Saving and loading ROIs 3 10 4 1 Saving ROIs 3 10 4 2 Loading ROIs 3 10 5 Editing ROIs 3 10 5 1 Selecting ROIs 3 10 5 2 Annotation and labelling 3 10 5 2 1 Annotating an existing ROI shape 3 10 5 2 2 Labelling Images 3 10 5 3 Moving or resizing a single ROI 3 10 5 3 1 Moving a single ROI shape 3 10 5 3 2 Resizing a single ROI shape 3 10 5 4 Changing the appearance of an ROI shape 3 10 5 4 1 Adjusting display of annotation text 3 10 5 4 2 Adjusting display of the ROI shape 3 10 5 4 3 Hiding ROI shapes 3 10 5 5 Deleting a single ROI shape 3 10 5 6 Editing multiple ROI shapes and ROIs 3 10 6 Viewing ROI information 3 10 6 1 Viewing summary ROI information 3 10 6 2 Measurement results 3 10 6 2 1 Showing summary results 3 10 6 2 2 Refreshing summary data 3 10 6 2 3 Saving summary data 3 10 6 3 Viewing pixel intensity values 3 10 6 3 1 Graphical view 3 10 6 3 1 1 Configuring the Graph view 3 10 6 3 1 2 Saving graphical views 3 10 6 3 2 Intensity View Copyright 2006 2007 University of Dundee All Rights reserved Page 83 OMERO clients User Guide 3 10 1 Accessing the Measurement Tool Assuming the image on which you wish to perform measurement is currently open in the Image Viewer you can open the Measurement Tool by one of two ways e Clicking on the measurement tool icon Ti in the main Image Viewer toolbar above the image or e Open the Controls menu select Measurement This will launc
72. serwer Cancel mport Figure 2 3 2 import window showing images destination and filename options To import images into OMERO 1 Log into OMERO importer The application will open a window similar to that shown in Figure 2 3 1 2 Use the File Viewer panel to browse and select one or more images you would like to import 3 Add the selected images to the list of images for importing referred to as the Import Queue by selecting the plus button 4 The import window appears see Figure 2 3 2 prompting you to select a Project and Dataset this will be the destination on the OMERO server for the imported images In this window you can a Select an existing Project and Dataset from the menus shown if you have previously created them in either OMERO importer or OMERO insight b Or for first time OMERO users use the Add button to create a new Project You can then create a new Dataset in your new Project or a new Dataset in an existing Project c The bottom half of the import window see Figure 2 3 2 also allows you to select a filename from one of three options i the short file name e g mylmage dv ii the full path name e g c important_work stuff mylmage dv iii the short file name plus a number of leading directories e g if you choose to add one directory to the directory c important_work stuff mylmage dv your final imported image would be named stuff mylmage dv Copyright 2006 2007 Unive
73. shape to be propagated Open the ROI Assistant by selecting the ROI Assistant button Ry The ROI Assistant shows the timepoints and z sections in which the selected ROI shape currently appears with the symbol of the ROI shape s type see Figure 3 10 3 4 1 which shows an elliptical ROI shape Click on ROI shape symbol and drag it across the z sections or timepoints into which you wish the shape to be copied Selected timepoints or z sections will be highlighted see Figure 3 10 3 4 2 Make sure the Add ROI radio button is selected Select the Close button The ROI shape and any accompanying information including annotations see Section 3 10 4 will now be propagated across the selected z sections or timepoints The ROI Assistant can also be used to remove ROI shapes from selected z sections or timepoints by following the instructions above but selecting the Remove ROI checkbox Copyright 2006 2007 University of Dundee All Rights reserved Page 91 OMERO clients User Guide Urari dare Devkic Tia ae T ape ADi Asisiitis 2s hrdusgh brie td fie etd LT EET Ha a 4 L gt o Shape Tri Coen Dettori pies Y Coed r Teg Pi ACi Assina alews piu ti crete aa REH which daliri Clive add acy Rinia AD l Width Hig Figure 3 10 3 4 1 Propagating ROI shapes e g an elliptical ROI shape with the ROI Assistant Copyright 2006 2007 University of Dundee All Rights reserved Page 92
74. size View one thumbnail at a time in a container Click on the Switch to Single view mode button The display changes to show only one thumbnail in the selected container To change the thumbnail currently in view 1 Click the Switch to Single view mode button again 2 Choose the Select option from the menu appears 3 Then select the filename of the image you wish to view from the submenu that appears 4 The displayed thumbnail changes To return to viewing multiple thumbnails 1 Click the Switch to Single view mode button again 2 Choose the Multi view mode option from the menu that appears 3 You will now see all thumbnails in the container Collapse a container Click on the Collapse button at the top of the container you wish to collapse This will temporarily remove all thumbnails from view and reduce the size of the container Click on the same icon again it is now an Expand button to bring the thumbnails back Copyright 2006 2007 University of Dundee All Rights reserved Page 129 OMERO clients User Guide Copyright 2006 2007 University of Dundee All Rights reserved Page 130 OMERO clients User Guide 3 11 2 2 Display Tree View of images Selecting the Display Tree View option opens a pane where you can view the files currently shown in the Hierarchy Viewer as a tree structure much like the left hand pane of the Data Manager When the Tree View is visible select the Display Tree View button again
75. ta Managet cccssssssseeceeeeeeeseeceeeeeeenseeneeaeees 21 3 2 Viewing and editing user account details ssssseeeeeeeeeeeeeeeeeeeees 23 3 3 Managing projects and datasets cccseessseeeeeeeeeseseeeeeeeeeeeseeeeeeeees 24 3 3 1 Creating projects and Adatasets ccccccseeeeeeseeensesssscsseeseeeeeeeeeeeees 25 3 3 2 Renaming projects or dataSetS sssecccceeseesseeeeeeeeeeeeeeeeeeeeeeeees 29 3 3 3 Removing projects or datasets ccceessesseeeeeeeeeeeeeeeeseeeseeeeees 30 3 3 4 Expanding a project to see constituent datasets 31 3 3 5 Expanding a dataset to see constituent images cccsseeeeeeeees 32 3 3 6 The Projects Categories and Images tabS scssseeeeeeees 33 3 4 Viewing other people s images eeeeceeeeeeeeeeeeeeeeeeeseeeeeeeeeenseeeeeeeees 34 3 5 Additional information about projects datasets and images 36 JO SARNGTIIONS siitinscneticcricanates iinet iinininnainnemeeiedes 37 3 6 1 Viewing annotations sisinio aisinas arradan 38 Copyright 2006 2007 University of Dundee All Rights reserved OMERO clients User Guide 3 6 2 Annotating a single image or dataset cccccccceeeeeeeeeeseeseeeeees 39 3 6 3 Annotating multiple images or datasets ccccessseneeeeeeeees 40 3 7 Categorising IMAGOS iiis ainai 42 3 7 1 Creating category QlOUPSsicccisesicssninnnanenciniatnscapsn
76. tegoret 11 T B Denat 1 2 Sy Tes brages Jopi disuse 38 ersi Dep o ese beep Pap Sok pre Figure 3 8 1 2 Truncated image Figure 3 8 1 3 Full image pathname pathname The actual number of directories shown in the full image pathname depends on the option chosen when importing the image using OMERO importer Copyright 2006 2007 University of Dundee All Rights reserved Page 52 OMERO clients User Guide wy This option expands to reveal a menu with further options for viewing images discussed in more detail in Section 3 8 2 It is only visible when the Images tab is selected This option allows you to quickly collapse the current list of image filenames to show only parent projects or category groups If at any time the left hand display appears not to be showing the information you expect select z or Refresh Current Tree from the File menu to refresh the display Copyright 2006 2007 University of Dundee All Rights reserved Page 53 OMERO clients User Guide 3 8 2 Retrieving selected images You can retrieve selected images from your collection of imported data by filtering out images based on the categories they belong to or by datasets Filter images Retrieval Filter images retrieval al Select itema in the fallowing list Limit the images retrieval by selecting items in the following Nise oF daragers l Ba empi ME temp Bi TesDatasetl Ea Tespa Select All Deselect All Apply Canc
77. tegory group Multiple projects or category groups Multiple projects or category groups Multiple humbnail containers one for each dataset in each project category group see Figure Figure 3 10 1 Table 3 10 1 Image selection method in Hierarchy Viewer display The Hierarchy Viewer offers an alternative layout Flat Layout option This is a flat grid display of all displayed thumbnails with no containers To select your preferred layout option open the View menu select Layout and choose between Flat and Hierarchical Copyright 2006 2007 University of Dundee All Rights reserved Page 124 OMERO clients User Guide dik gg Ias tath Areca 2 a ariji Fh Bats Cobos teal 17 HE00 HEE E aici wt 7 ET E La F EF DORR E Bees F JE T r je Fi i BODO eee oo TF do O Cee Reel Tobe 6G it a Figure 3 10 1 Hierarchy Viewer showing multiple containers 3 11 1 Viewing an image from the Hierarchy Viewer 3 11 2 Using the Hierarchy Viewer 3 11 2 1 Adjusting thumbnail display 3 11 2 2 Display Tree View of images 3 11 2 3 Sorting images 3 11 2 4 Managing images in the Hierarchy Viewer 3 11 2 5 Additional image information the Working Area Copyright 2006 2007 University of Dundee All Rights reserved Page 125 OMERO clients User Guide 3 11 1 Viewing an image from the Hierarchy Viewer Once you see thumbnails in the Hierarchy Viewer you can view an individual image in more detail in the Image Viewer thr
78. the histogram and line profile if shown will be automatically updated to reflect these changes 3 10 6 3 1 1 Configuring the Graph view 3 10 6 3 1 2 Saving graphical views Copyright 2006 2007 University of Dundee All Rights reserved Page 119 OMERO clients User Guide 3 10 6 3 1 1 Configuring the Graph view To change the magnification of the Graph view right click on the histogram or line profile This brings up a menu that allows you to e Apply a zoom in or zoom out effect to the data by changing the visible values of the x and or y axes increasing or reducing the range of values shown in the graph e Apply an automatic scaling effect so that the ranges of the x and y axes accommodate exactly the maximum and minimum values of the intensity data of the ROI shape in question If the selected ROI shape is part of a multidimensional ROI slider bars will be provided to allow you to move through each timepoint and or z section in a similar way to the Image View window In the example shown in Figure 3 10 6 3 1 1 the vertical slider bar to the left of the figure allows you to change the z section for which the intensity data should be shown Copyright 2006 2007 University of Dundee All Rights reserved Page 120 OMERO clients User Guide 3 10 6 3 1 2 Saving graphical views The graphs shown can be saved as images Right click on the graph to be saved Choose the location of the image file to be saved Select the S
79. tions shown see Figure 2 4 1 2 e Split View showing each channel as a separate image for multi channel images plus composite image side by side see Figure 2 4 1 3 You can view more than one image at the same time each will open in a separate Image Viewer window mv WaAsncuton spe Ea F ann ia Dard Saen i New snnataion D Nee amoaton gt 2007 05 17 22 35 35 2007 05 17 225535 check this agen Total 1 annotatior Onete Seve 2 2 3 1 0 0 i ar T Figure 2 4 1 1 Image Viewer Standard Figure 2 4 1 2 Image Viewer Annotation View View Copyright 2006 2007 University of Dundee All Rights reserved Page 10 OMERO clients User Guide Mew amao in Figure 2 4 1 3 Image Viewer Split View 2 4 1 1 Viewing z sections or timepoints 2 4 1 2 Adjusting channels 2 4 1 3 Additional viewing options Copyright 2006 2007 University of Dundee All Rights reserved Page 11 OMERO clients User Guide 2 4 1 1 Viewing z sections or timepoints For images with multiple z sections or timepoints OMERO allows you to easily view these manually or automatically To manually view composite z sections or timepoints for an image in the Image Viewer window all three views e Use the vertical Z slider to manually view individual z sections e Use the horizontal T slider to manually view individual timepoints Or open the Controls menu and select the Movie option to open the Movie Player Here you can
80. tionship with datasets Images in OMERO are inherently multi dimensional they consist of pixels across the usual three spatial dimensions and can include multiple colour channels and time series Copyright 2006 2007 University of Dundee All Rights reserved Page 145 OMERO clients User Guide Copyright 2006 2007 University of Dundee All Rights reserved Page 146
81. ton again Copyright 2006 2007 University of Dundee All Rights reserved Page 135 OMERO clients User Guide 3 12 Managing windows in OMERO insight As you work with images in OMERO insight you may end up with several open windows The Windows menu available at all times shows all windows you have currently open in OMERO insight and allows you to jump between windows Copyright 2006 2007 University of Dundee All Rights reserved Page 136 OMERO clients User Guide 3 13 Closing OMERO insight To end a session using OMERO insight open the File menu in the Data Manager and select Quit the Application or close the Data Manager window Whenever you attempt to start a new action without saving edits or additions you will be prompted to save or cancel the changes you made Copyright 2006 2007 University of Dundee All Rights reserved Page 137 OMERO clients User Guide 4 Feedback reporting 4 1 Help Information 4 2 Feedback Facility Copyright 2006 2007 University of Dundee All Rights reserved Page 138 OMERO clients User Guide 4 1 Help Information Help information is not currently available through the Data Manager Help menu but you can send feedback by opening the Help menu and select Send Comment Copyright 2006 2007 University of Dundee All Rights reserved Page 139 OMERO clients User Guide 4 2 Feedback Facility This Beta version of OMERO importer and OMERO insight has b
82. tton Pa 2 Move the mouse pointer to the area of the image at which you want to start drawing the line 3 Hold down the mouse button and drag the mouse pointer to the point you wish to finish the line 4 Release the mouse button the line is now created The length of the line will be shown along with the angle of the line to the horizontal see Figure 3 10 3 2 2 To draw a connecting line between two ROI shapes Select the Line toolbar button 1 2 Click inside or on the first ROI shape you wish to connect 3 Click inside or on the second ROI shape you wish to connect 4 Aconnecting line will be drawn between the two ROI shapes see Figure 3 10 3 2 3 Copyright 2006 2007 University of Dundee All Rights reserved Page 88 OMERO clients User Guide To draw a freehand line scribble 1 Select the Scribble toolbar button w 2 Move the mouse pointer to the area of the image at which you want to start drawing the line 3 Hold down the mouse button and drag the mouse pointer to form the line 4 Release the mouse button the line is now created To draw a polygon 1 Select the Polygon toolbar button Q 2 Move the mouse pointer to a point on the image at which you want to start drawing the polygon 3 Hold down the mouse button and drag the mouse pointer to create the polygon shape 4 Release the mouse button the polygon is now created Figure 3 10 3 2 1 Point ROI Figure 3 10 3 2 2 Line ROI
83. tton becomes a Pause button I Copyright 2006 2007 University of Dundee All Rights reserved Page 74 OMERO clients User Guide 3 9 4 2 Selecting z section and timepoints A third option for viewing different z sections and timepoints exists when an image is shown in Standard View and Annotation View Holding down the mouse button and dragging the mouse vertically up or down the image moves through z sections dragging horizontally moves through timepoints Dragging diagonally will simultaneously change z sections and timepoints Copyright 2006 2007 University of Dundee All Rights reserved Page 75 OMERO clients User Guide 3 9 4 3 Additional Movie Player options for z section and timepoint viewing The Movie Player allows you to make additional adjustments to the movie being played To configure how the movie is played the Play menu gives you several choices e Forward shows each z section or timepoint in turn once only e Backward shows each z section or timepoint in turn once only but in the opposite order to Forward e Loop shows each z section or timepoint in turn Forward but continuously until you choose to stop the movie e Loop Backward shows each z section or timepoint in turn Backward but continuously until you choose to stop the movie e Back and Forth shows each z section or timepoint in turn Forward and then Backward until you choose to stop Table 3 9 4 3 1 shows the difference in the Play o
84. ty of Dundee All Rights reserved Page 59 OMERO clients User Guide 3 9 1 Viewing a specific Channel The channel buttons shown as the four coloured squares labelled 457 528 617 685 in Figure 3 9 1 enable you to turn on or off specific channels for multi channel images Turning on or off a channel will result in an immediate visual change to the image shown in the Image Viewer The colour band selected for a given channel corresponds to the emission wavelength of the channel If this information is not available the channels will be mapped to red green and blue The colour used to display any channel can be customised using the Colour Picker Section 3 9 2 Channels can be turned on or off by clicking the relevant channel selection button aligned vertically on the left edge of the Image Viewer window Buttons show the colour associated with the channel plus wavelength in nanometres if this information is available Copyright 2006 2007 University of Dundee All Rights reserved Page 60 OMERO clients User Guide 3 9 2 Additional viewing options 3 9 2 1 Colour and greyscale viewing 3 9 2 2 Movie viewing across channels 3 9 2 3 Channel configuration 3 9 2 4 lmage information 3 9 2 5 Annotation View Copyright 2006 2007 University of Dundee All Rights reserved Page 61 OMERO clients User Guide 3 9 2 1 Colour and greyscale viewing The top two Image Viewer toolbar buttons change appearance depending on the curr
85. undee All Rights reserved Page 134 OMERO clients User Guide can add additional annotations or delete an annotation you have previously entered For more details see Section 3 6 This tab is selected if you click on the Annotation icon for a thumbnail 2 Categorisation This enables you to see the categories the currently selected image belongs to You can then declassify the image s categorisation in a similar way to the Data Manager see Section 3 7 This tab is selected if you click on the Categorisation icon for a thumbnail To categorise an image or collection of images you need to use the Edit menu 3 Find This feature enables you to search within the selection of images shown in the Hierarchy Viewer The find works in a similar way to the Data Manager Find feature discussed in Section 2 8 2 Results are displayed in the Results panel to the right of the Find form 4 Editor This enables you to view and edit Properties and Permissions information see Section 2 5 for more details 5 Info Shows additional information about the image including Number of pixels along X and Y axes Number of z sections Number of timepoints Size of a pixel in microns Emission wavelengths if available papo The Working Area can be set to automatically show information for any thumbnail when the mouse pointer hovers over that thumbnail To enable this functionality select the button To stop this behaviour select the but
86. unnnnnnnnnnnnnnnnnnnnnnnnnn 63 3 9 2 3 Channel COMMMQUIANOM saciercicctasasdandenctcnctondessssnattencssenaienduanennies 64 3 9 2 4 Image INTOMMANOM sais svainsiannidessanasancesciinieannnsnacdannsavixaninieduabananannia 66 3 9 2 5 Annotation VICW ciisiiiasancisiniociiasiiwadartteeiatrinadniibaniarbdctinieunduiats 67 3 03 MAGHIICATON siiariasniasicurdeesintinnrndlintieerieniciiuaneriniddi nen sinalassdnihis 68 3 9 3 1 Magnifying the Whole image ccsssseeeceeseeseeneeeeeeeesseeeeeeees 69 3 9 3 2 Magnifying an area of the iMage cccssseseeeceeeeeeseeeneeeees 70 39 3 3 DOAIS DAP sv crnsneicnnesnsncrinasccnnnendannsnansiansnnehdaeussnssasnantdeansaniiataniadianune 72 3 9 4 Viewing Z Sections and tiMePOiNts cccseesseeeeeeeeeeeeeeeeeeeeeeees 73 Copyright 2006 2007 University of Dundee All Rights reserved OMERO clients User Guide 3 9 4 1 Automated viewing of z sections and timepoints 74 3 9 4 2 Selecting Z section and tiMePoOiNts ccccceseseeeeeeeeeeeeeeees 75 3 9 4 3 Additional Movie Player options for z section and timepoint VIEWING iriiria asarana aaraa aaa a a aa A aaa a aa aAa Eaa adaa aaa 76 3 9 5 Image Rendering Options ssccisccicesisisissadanicccisisiaxadsnascctscetieziendivadannns 78 3 10 Introduction to the Measurement Tool ssseeeeeeeeeeeeeeeeeeeeeeeeeeeeees 82 3 10 1 Accessing the Measurement Tool ccsssseseeeeeeeeeeeeeeeeeeeeeeees 84
87. vanced tasks are described in 2 1 Installing OMERO importer and OMERO insight 2 2 Logging in 2 3 Importing images 2 4 Viewing images 2 4 1 Viewing a single image 2 4 1 1 Viewing z sections or timepoints 2 4 1 2 Adjusting channels 2 4 1 3 Additional viewing options 2 4 2 Viewing a selection of images the Hierarchy Viewer 2 5 Saving images Copyright 2006 2007 University of Dundee All Rights reserved Page 2 OMERO clients User Guide 2 1 Installing OMERO importer and OMERO insight Latest versions of OMERO importer and OMERO insight are available for download from http trac openmicroscopy org uk omero wiki Milestone Downloads Once you have downloaded the OMERO importer and OMERO insight installer packages double click the packages to start the install process Copyright 2006 2007 University of Dundee All Rights reserved Page 3 OMERO clients User Guide 2 2 Logging in The log in procedure is the same for OMERO importer and OMERO insight When you start OMERO importer you will be asked to log in See Figure 2 2 1 The administrator who set up OMERO can provide you with a user account and the address of the OMERO server where your images will be stored You provide the address of the OMERO server by selecting the button and entering the details in the form provided ORT Mat rocopy mn inne apen Microscopy ermironment OMERO importer OMERO insight eae Log in ee I os Lea i re Figur
88. ver the thumbnail to be magnified An enlarged version appears 3 If you have a mouse wheel you can increase or decrease the magnification factor by scrolling the wheel Continuous movement of the mouse pointer will magnify in turn each image the pointer passes over To keep a specific thumbnail on screen 1 Select the pin up icon g 2 The thumbnail will now remain on screen regardless of the position of the mouse pointer If you have a mouse wheel you can increase or decrease the magnification factor of the pinned thumbnail by scrolling the wheel To remove a pinned up thumbnail 1 Select the Close button E at the top of the thumbnail window 2 The pinned up thumbnail is removed from display Copyright 2006 2007 University of Dundee All Rights reserved Page 128 OMERO clients User Guide Closing the Hierarchy Viewer window also removes all pinned up thumbnails Change the size of all thumbnails in a container You can enlarge or reduce the size of each thumbnail in a selected container this includes all thumbnails in sub containers To increase the size of all thumbnails 1 Select the container 2 Select the Zoom In All Images button A To decrease the size of all thumbnails 1 Select the container 2 Select the Zoom Out All Images button a To reset the size of all thumbnails 1 Select the container 2 Select the Reset Thumbnail Size button 3 Thumbnails will return to the default
89. way to the Find in Page feature provided by many Web browsers It allows you to search for a text string within all items displayed in the left hand pane Figure 3 8 3 1 rrii Ghain pa Diala Mirnij ager g an Wh Sdn Utes file Cha baa Ted ages Oh ie T e ns Hrem i nni ger byin D 14 harma Diar pia Dwear E m e i in Coates Gj Hee one gal r krr aj E PA thii T hj tet aP o Iri aghi iii El tet rape ie E Chins II T ld Termes Tent wap bht HAm I T A Draci EN Praga bee hy eS ir a Tied EHA D Toe Aa Pree kash caie CL ecereee fard Figure 3 8 3 1 Find in Tree request showing results To conduct a search 1 In the Edit menu select Find in Tree A form will appear at the bottom of the Data Manager window Type the text string you wish to search for in the Find text box Use the arrow icon to select whether you wish to find a pattern in image names or descriptions The Match Case checkbox can be checked if you want to ensure that image filenames are returned only if they match the case of the text string you specify The search will be dynamically conducted reporting how many images were found that match your search criteria The first image found will be highlighted Figure 3 8 3 1 use the Find Next or Find Previous buttons to move through each image found If no images are found a Phrase Not Found message is shown Copyright 2006 2007 University of Dundee All Rights reserved
90. y E EN Lm pe pe pe e dks i fi E Figure 2 6 2 1 Adding an annotation to an image You can also add an annotation to an image in the Image Viewer see Section 3 9 2 5 and in the Hierarchy Viewer see Section 3 10 2 5 Copyright 2006 2007 University of Dundee All Rights reserved Page 39 OMERO clients User Guide 3 6 3 Annotating multiple images or datasets OMERO allows you to add an annotation to a selection of images or datasets all at once To do this 1 Select the images or datasets Select the toolbar icon E 3 This opens up the Annotate dialog box see Figure 3 6 3 1 It shows you in three panes a the list of images or datasets selected b atree view showing names of users who have added annotations expanding a user name shows the time of each annotation added c space to add a new annotation or see the text of any existing annotation 4 Enter the annotation text in the right hand pane 5 Select Save a message box appears see Figure 3 6 3 2 Choose the All option to save the annotation for all selected images or datasets or One to save the annotation for only the first selected item the one named in the message box ane Anea k Anmar tha rel bed nema E amnp ation for babiinwt lt 0 tubhivat Ci TEPO a Jed LTP oy a jibag kka sangap 3 hah feb Ce TPE Y i Dasi Haia 0 mhiar iD freee CF TP ar gt Kpa a ner Clove Figure 3 6 3 1 Annotating multiple it

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