IUL Flash & Grow 1.2 User Manual - Cole
Contents
1. e A double click in the image will alternately show Processed and Captured image to help evaluating the colony layer e A right click on the image shows a context menu with the options you have to select or zoom images and to split the image panel These features are explained in detail in part 6 of this manual but most of them are self explanatory You can o Zoom to better select specific colony or background shades o Split the panel to see Captured and Processed images side by side or to have panels with different zooms 3 1 1 Capture Image e With the Edition Dialog in the Image Capture page place a typical well populated plate on the Flash amp platform and push the white button there You Il get a Captured image of your plate e Adjust the light and exposure settings to get the clearer contrast between the colonies and the background of the plate Any time you change a light setting a new image will be captured showing the effect you get 3 1 2 Set the Plate Diameter e In the Captured Image click and drag on the blue circle to fit it to the inside area of the plate That circle will help to keep track of the whole plate area size and is used by the process to calculate the volume corresponding to the counted part of the plate in case of pour plate processes 24 3 1 3 Set the Colony Layer Filter After image capturing click the Next Page button below the dialog to get the Colony Laye2. e In the top sub panel the existing Work Sheets are shown You can select any to get it open in the lower sub panel e Right click on the lower sub panel and select o Edit To edit the currently selected sheet o New To create a new sheet o Import To import a sheet from an XML or CSV file o Export To export a sheet to an XML or CSV file e While editing or creating a new sheet you can o Read barcodes to fill the Plate Identifier field in the currently selected row o Drag and drop the Operation Settings name from the Operations Folder to fill the Plate Operation field in the currently selected row Click on the Operations Folder button to get it visible 51 6 4 Calibrating the Flasha to Work in the Plate Handler When the Flash amp works integrated in the Plate Handler it doesn t have the centering springs that ensure plate centering in normal operation In this case the plate positioning in the Flash amp platform is done by the Handler hand Thereafter the fine centering of the image must be done with a plate or a calibration pattern placed by the Handler Let s see the steps for doing it In the Handler Program dialog select Handler Stop to Plate If you don t have a running Handler Program start one we ll only get the Handler in the plate dropping position When the Handler stops you can change the plate in the Flash amp platform by an appropriate plate contain
3. Run Dialog To make settings not included in the Run Dialog available at each plate the Operation must be customized to show the Input Dialog When enabled the Input Dialog pops up at each plate run showing and allowing to change all the settings assigned to the General Input or the Group Input categories for that Operation The user can change or accept those values as it does with the settings in the Run Dialog To enable the Input Dialog e Go to the Options page of the Customization Dialog e Set InputDialog to true This option is by default a Group Setting That means the Input Dialog gets enabled for all the Operations of the same type as the current Colonies or Halos If you want only a specific operation to show the Input Dialog you must change the category of InputDialog to Specific before enabling it 42 5 2 4 Customizing the Results Table The format of the results table is specified by the ResultTableFormat parameter in the Options page of the Customization Dialog By default the ResultTableFormat is a Group Setting what means that the same table format is shared by all the operations of the same type If you want special tables for specific Operations you must first change the Scope of that parameter in such Operations to Operation Specific Editing the ResultTableFormat opens the Resul
4. a tool bar allows for normal actions during the edition change page save or restore and get context related help Each page in the dialog will be a step in the process of optimizing the new operation settings Hints e You can save your settings any time by clicking on the Save Changes button and giving an appropriate name or restore the initial or the last saved settings by clicking on the Undo Changes button e A double click in the image will alternately show Processed and Captured image to help evaluating the colony layer e A right click on the image shows a context menu with the options you have to select zoom or split the image panel These features are explained in detail in part 6 of this manual but most of them are self explanatory You can o Zoom to better select specific inside outside shades o Split the panel to see Captured and Processed images side by side or to have panels with different zooms 4 1 1 Capture Image e With the Edition Dialog in the Image Capture page place a typical plate with halos on the Flash amp platform and push the white button there You ll get a Captured image of your plate e Adjust the light and exposure settings to get the clearer contrast between the halos contour and the background of the plate Any time you change a light setting a new image will be captured showing the effect you get 4 1 2 Set the plate diameter e In the Captured Image cl
5. e The Round and Interpolate controls are used when part of the halos contours are not detected or are not round enough to be accepted but can be guessed from the rest e Higher values of the Round parameter give priority to halos roundness forcing more interpolated parts of the contour in case of not round enough halos e The Interpolate parameter puts a limit to the part of a contour that can be guessed If the guessed parts of the contour needed to fit roundness or to fill contour gaps are more than the specified percent the halo will not be valid 4 1 6 Identify the Operation with Name and Icon When settings seam to be correct click the Next Page button to get the Name and Icon page that will serve to identify that operation Set the name and select an icon according to your preferences 34 The Next Page button is now named Run Operation If you click on it and the current operation settings are not saved you will be asked to save the operation Do it now by clicking on the OK button A button with the selected icon and name will appear in the Operations Tool Bar below the working area That s the button you Il use to recall those settings any time you need it The dialog switches to the Halos Run Data page That s the dialog with the operation data that can be changes in a plate per plate basis We ll come back to that dialog in the next chapter To
6. Handler Control buttons are the three buttons that substitute the Run Operation buttons while in Handler Program mode The primary function of those buttons is very straightforward Handler Run Button Click on the handler run button to start running the Handler Program in the current rack or continue with it after any pause 48 Handler Pause Button Click on the Handler Pause button to stop any currently running Handler Operation The Handler operation will also stop any time an error is detected the carrousel door is opened or the program reaches a preset stop point In any case you must click on the Handler Run button to continue the operation Handler Home Button The Handler Home position must be reached any time you change or remove the plates rack and also before switching off the Handler even in case that the process must be continued in the current rack In home position all the plates are back in their original positions in the rack and the Handler is at rest empty of plates Moving to the Handler Home position may be done any time during the rack processing The Flash amp Grow keeps all the Handler Program settings and plate position and count to continue at the point it was interrupted 6 2 3 Additional Handler Operations The Handler Run and Handler Home buttons do have drop down lists what are used to call some less frequently used but useful f
7. in the image may be changed If yellow is not adequate for your plates see part 5 below for instructions on how to customize the operations 3 1 4 Set the processed image diameter The yellow circle in the Processed image marks the limits of the processed part of the image The processed image will be normally smaller than the total area marked by the blue circle to let out the borders of the plate where the media curvature interferes In any case the process calculates the sample volume corresponding to only the counted area getting the correct colony concentration result To adjust the processed image diameter e In the Processed Image click and drag on the yellow circle to let out of the processed area any reflections or other irregularities related to the borders of the plate 3 1 5 Shape and Size Filtering When the colony layer seams good enough click the Next Page button to get the Shape and Size Filter page The Processed image will show now small red crosses marking the center of every identified colony e You can select here the minimum and maximum diameter of your colonies to help differentiating there from other spots in the image e If your plates are inoculated using a spiral platting instrument check the Spirally Inoculated box in the dialog The pattern of white circles signals the areas corresponding to the different spiral platting densities and in case that the plate is populated enough on
8. result of the process If any problem arise that s immediately seen and corrective measures can be taken After the last plate is processed you must push once more the white button to get the last results accepted 2 2 2 Identifying Your Plates with Barcode Labels If your plates are identified with a barcode label you can enter the plate identifier directly from the bar code reader If you have a barcode reader that emulates keyboard entry using it is of course transparent to the application You proceed as when you type the identifier but instead of typing you read the barcode If your bar code reader must be connected to a serial channel in the host computer the application must be aware of it In this case e In the Settings menu select Environment e In the Environment Settings Dialog set the Barcode Reader settings according to your device e Close the dialog clicking on the OK button e Inthe Main Tool Bar click the Barcode button While Barcode button is pushed the auto incremented default for the sample identifier is no more present The Sampleld field will remain empty waiting for a barcode entry Using a barcode reader is yet compatible with keyboard entry If a label can t be read you can type the identifier by hand and go ahead 17 2 2 3 Processing from the Host Computer As described above the routine work to apply the same operation to a collection of similar
9. the Operation SettidgS cooonoccconncoconocncooncnononcnononanononanonnnnnos 15 2 2 Plate PIOCESSINS iio 17 2 21 Route Plate Process ados 17 2 2 2 Identifying Your Plates with Barcode Labels oooooooccnnccinccnnncnnocononnnnnncnnnoos 17 2 2 3 Processing from the Host Computer ds 18 2 2 3 1 Run Accept Cancel BUON is 18 2 2 3 2 Trying Different Operation SettidgS oooooconocononcnoncnnncnconncconncnnnnona cono nccnncnnnos 18 2 2 33 Usa Bfawinz Lol india 18 25 gt Result Data io RAA 20 ES SN A A 20 2 32 Review saved IA Ti RATE 20 ZO REDEOCESS Saved MAS os 20 2 3 4 Data and Image HO ita 21 2 3 5 Exporting Data Tables inicias 21 2 3 6 Exporting Operation Mire A ida 22 Pat o ERZE 23 COMUNE Colonies E dde 23 3 1 Create the Colony Count Operation Settings ooooocnnccccnoncccnonncconancnonnncnnnnanonancninnnos 24 IMA Capture Ad cid 24 Dol sere te Plate Dd e lo oa 24 3 1 3 Set the Colony Layer Filter cin tenias 25 3 1 4 Set the processed image diameter AA ARA eae 26 SL O O AO 26 3 1 6 Identify the Operation with a Name and an Icon and Save 27 3 1 7 Setting up More OperAliONS wd EEG GWO YE 27 3 2 Colony Counting Operation Run says WYL Ad 28 3 2 1 Select the Operation You Wan uwaa id dok DAD EA 28 3 2 2 Process Your Pl iR tor 28 3 3 Improving Your Colony Count Results Interactively oooooconnnocccnoncccnoncccnanccnnnnos 29 3 3 1 Add colonies to the could 29 3 3 2 Remove co
10. unselect the process click on the pushed operation button or simply go ahead with another operation You Il be asked to confirm that the current operation should be canceled Click Yes as far as the results for that plate are not to be saved by now 35 4 2 Halos Measure Operation Run 4 2 1 Select the Operation You Want Select the Operation adequate for your plates from the Operations Tool Bar below the working area If you are not sure don t bother you can change it later The pilot in the Flash amp will stop flashing indicating it s on line and the Operation Run Dialog will open Note that by default the Sample Identifier field will get incremented at each new measure or left blank in case that barcode reader is active Results Table Name and Remarks will keep their last values Change as needed any of those values 4 2 2 Process Your Plate Place the plate in the Flash amp platform and push the white button there You II get the processed image of that plate The halos painted in semitransparent red and the valid ones numbered according to their position in the plate Observe if the halos had been correctly detected If you agree go ahead If not you can try slight changes in threshold or interactively correct the measures The next chapter explains how to use the tools available to interact with the process If everything is correct proceed to the next plate by simply placing the plate in the Flash
11. yet accurate enough and then click the Accept button in the main tool bar Calibration is done 13 Part 2 Basics of Using the Flash amp Grow 2 1 Operation Settings This chapter is only a short introduction to general aspects of the operation of the Flash amp Grow Next two chapters are step by step guides to set up colony count and halos operations and run them on your plates Chapter 3 is devoted to colony counting chapter 4 to halos measuring Both chapters are self contained guides For a fast start up you can go directly to whatever is your primary interest there and skip this chapter Nevertheless a previous general overview of how the Flash amp Grow operates may help understanding their logic and the sense of each term as it s used in the next chapters Giving such an overview is the purpose of this chapter Flash amp Grow supports three types of standard operations Calibration Colony Counting and Haloes Measuring We call an Operation the process of capturing an image and getting some results from that image through processing and or user interaction and finally if they are accepted storing results altogether with additional information as identifiers and comments in a table for future use and recall Operations are driven by setting the values that control their behavior A complete set of setting values for an operation is what we call the Operation Settings for that operation For Colony Counting
12. 7 4 3 4 Restore a previously removed halo ooooonocccnoncccooocccnoncnononanononcnononcconnncconnnos 37 A SERATO OR A i OE RAE 38 Customizing he Flash 66 Grow siasio dia caia 38 5 1 Customize the Operations Toolbar ee seeeo oe aaa eee aaa ea aaa aaa eeaaaaecca 39 5 1 1 Unlock and Re Lock the Operations Toolbar Configuration 39 jl Change Buttons Order esto ate Madey nk OPRAWA NAA 39 DLs REMOVE a RUMOR lt A Oe Bek eae Be TE PAREAN 39 5 1 4 Remove an Operation from the Button List ooooononcnnnnononcnnnconocncnoncnonananncnnnoo 39 5 2 Customize the Operation Settings ooooconncccnoncccnoncccnnnnnonnncnononcnonnncnnnnncnononcncnnnncnnnnos 41 5 2 1 Changing Setting Valles minita diaria prada 41 5 2 2 Changing the Scope of Parameter Values ooooconnnococnoncccnoncncnoncnononcconnnanonnnanos 42 2 Using Dd R A A A AO Ak 42 5 2 4 Customizing the Results Table z ii LZ i a pal 43 A NO O R RAE 44 Using the Plate Handler ti ad 44 6 1 Install the Plate Handler with thee Flash amp Grow ocooooonoocccconccconcccconnccnnnnncnnnnncnnnnos 45 6 1 1 Activate the Plate Handler Flash amp Grow to Support the 1111111 45 6 1 2 Selecting the Serial Channel that Controls the Plate Handler 45 6 1 3 Testun C OMNECUO tt EA OR ATE DEE 46 6 2 Running the Plate Bandlera ROR aie ae Be A 47 6 2 1 The Handler Prostam neespri it ira 47 6 2 2 The Handler Cont
13. IUL Flash amp Grow 1 2 User Manual e RARE 1 Flash Grow 1 2 User Manval ts 1 MAAS c nnen AS a O EO EA 2 Part liusidanalc idad dai id 6 Sets Up The Application ts 6 Lh Installation Prerequisites A Oh RAA AO 7 1 1 1 Minimum Requirements for the Host PC ooconnccnocococcconanonanononononccnnncnnn ccoo nono 7 A O TON 7 1 1 1 2 Soap ic tee Mee led et eh ee ee a 7 1 1 2 Recommended Requirements for the Host PC cece eeseesseceeeeeeeeeeneeenaeens 7 Lal 2d Hardware A ene 7 T122 SoftWare ad 8 TES Supplied SoftWare tr dE GA GG EE R GE AZ A REA 8 12s Sottware I stallanto wa a ZAWOR AA E AE Bede 9 1 2 1 Installing the Flash amp Grow Application eeee se eee a aaa aaa aaa ena aaa eaaaaca 9 1 2 2 Installing the Camera Driver aa peana 9 1 2 3 Installing the Control Dri ver sg ae cada aw OG 9 1 3 Entering the Activation Keys e sens akit A AG c A AE 11 1 4 Configuring the Application Environment ee oeeee eee ea aaa aan wanna 12 1 4 1 Setting the Serial Channel that Controls the Flash amp Device 12 1 4 2 Protecting your Settings from Unwanted Changes 2 s 21s 211 22 12 1 4 3 Centering and Scaling the Image eee eesceceescecesececeeeeeceeeeeceeececseeeeesaeees 13 Pat tas 14 Basics of Using the Flash Gr W A A A ve Bes 14 Y A PEL 15 2 1 1 Edit and Customize Operation Settings eee eesecsseceeeeeeseeceaeceseeesneeenees 15 2 1 2 Save and Recall
14. Operation Settings that it was from the plate If you want a sample reprocessed from the saved image e Select the row in the results table and open the Operation Settings you want to run e Click the Run Button in the main tool bar Results of reprocessing an image can be added to a new row in the table or simply override the selected row By default the selected row gets overridden To change this feature you must set the ReviewToNewRow option in the Customizing Dialog to true 20 Note that by default ReviewToNewRow is a General Setting Thereafter changing that setting will affect all the operations If you don t want so you must change the Scope of ReviewToNewRow before changing its value 2 3 4 Data and Image Storage Configuring the Flash amp Grow Environment Settings gives different options for saving result data and images You can set DataFileName Here you can change the name of the file where Results Data Tables are saved Changing or renaming that file a new results environment will be created with new empty tables You can also restore a previous Results Data File by setting accordingly that file name DataFolder That s the folder where the Results Data File is saved and read from WorkFileName Here you can change the name of the file where Work Sheet Tables are saved Changing or renaming that file a new work environment will be created with new empty tab
15. To enter the appropriate channel in the Flash amp Grow Environment Settings 45 e In the Flash amp Grow main menu open Settings Environment Dialog e In the Plate Imaging Device section of the dialog set the Flash Connection field to the COM number the device is attached e Close the dialog clicking on the OK button 6 1 3 Testing Connections If installation and cable connections are OK the Handler activation key has been entered and the serial channel is correctly set you can start checking the Plate Handler from the Flash amp Grow application e Start the Flash amp Grow and turn on the Handler and the Flash amp switches e Inthe Main Toolbar click on the Plate Handler Mode button The Handler Program dialog will open at the left side of the working area in the same area that s used by the Plate Operation dialogs and the Run Buttons in the Main Toolbar will be substituted by the Plate Handler Control buttons Those dialog and buttons are explained in detail in the next chapter Now just for checking you ll only use the Handler Home button the right most of the Plate Handler Control buttons e Place a plates rack in the Handler carrousel close the shaft on the carousel to fasten the rack and close the door e Inthe Flash amp Grow click on the Handler Home button As far as the Plate Handler is already in its home position it should a
16. amp platform and pushing the white button Doing so will automatically save the current results and start a new operation on the new plate To change the operation settings simply select the new settings using the Operations Tool Bar To cancel the operation and eventually repeat from the beginning click the Cancel button in the Main Tool Bar Don t forget pushing once more the white button when you have done with your last plate to get the last operation results accepted If you try closing the operation or the application without doing so a dialog will ask for confirmation before canceling the current operation 36 4 3 Improving Your Halos Results Interactively After you have captured a plate image and get the halos measured a set of tool buttons gets enabled in the main tool bar Those buttons allow you to interact with the image to improve what the process has done by any of the following actions 4 3 1 Remove a halo that s not correct If any halo shows a wrong contour you can erase it from the image e Click on the Remove Halo button in the Main Tool Bar e Move the mouse cursor to left click on the halo you want removed 4 3 2 Draw a circular halo If a halo has been removed or not at all detected but the image allows you guessing how 1t really should be you can easily draw a circle to signal the area of that halo and get their diameter added to the results e Click on the Draw Circular Halo button in t
17. and Halos Measuring the Flash amp Grow maintains a collection of Operation Settings instances named and grouped according to their function each one adapted to a particular type of plates In case of Calibration there is a single set of settings that can be edited saved and recalled but remains unique 2 1 1 Edit and Customize Operation Settings To create or edit the Operation Settings a guided interactive process the Operation Edit Dialog working interactively with the image of real plates will help getting the best settings for each kind of plates After you have an Operations Settings created you can yet customize it using the Customization Dialog Changing the colors of graphic items or modifying the results table contents are examples of such customization The Customization Dialog will give access to all the settings available for that Operation both for selecting the different options available and for advanced tuning of some processes 2 1 2 Save and Recall the Operation Settings After the settings for a particular type of plates are defined in the Operation Edit Dialog they are assigned a suitable name and icon and a button is created in the Operations Tool Bar below the working area for easy recall Several Operation Settings may share the same icon in that case they are grouped under the same button that maintains a list of all of them and presents the las
18. ar Configuration To customize the toolbar you must first unlock it in the context menu e Right click with the mouse in the Operations Toolbar e In the context menu click Locked Configuration to uncheck that item When the bar is unlocked the buttons get grouped left side in the bar giving space to add or move buttons To recover the normal position of the buttons covering the whole bar you must re lock them e Right click with the mouse in the Operations Toolbar e In the context menu click Locked Configuration to let it checked again 5 1 2 Change Buttons Order To change buttons order e Click on the button you want moved and drag it to the desired position 5 1 3 Remove a Button To remove a button e Click on the button and drag it out the Operations Toolbar e Click Yes for confirmation in the Remove Button Dialog 5 1 4 Remove an Operation from the Button List To remove an Operation Settings out from a button list e Make sure the Operation Settings you want removed is the current selection for that button e Click on the button and drag it out the Operations Toolbar e Click Not in the Remove Button Dialog to avoid getting the whole button removed 39 e Click Yes in the Remove Operation Dialog to confirm you remove that Operation Settings Note If the deleted operation was the only one in that button the button will be also removed Empty buttons are not allowed To a
19. at plate The colony layer in yellow and the counted colonies marked with a red cross Observe what has been counted or not If you agree with the count go ahead If not you can try slight changes in the threshold or interactively correct the count The next chapter explains how to use the tools available to interactively improve the counting You can yet change any value in the Operation Dialog Results will be automatically updated If everything is correct proceed to the next plate by simply placing the plate in the Flash amp platform and pushing the white button Doing so will automatically save the current results and start a new operation on the new plate To change the operation settings you are applying simply select the new settings using the Operations Tool Bar To cancel the operation and eventually repeat from the beginning click the Cancel button in the Main Tool Bar Don t forget pushing once more the white button when you have done with your last plate to get the last operation results accepted If you try closing the operation or the application without doing so a dialog will ask for confirmation before canceling the current operation 28 3 3 Improving Your Colony Count Results Interactively After you have captured a plate image and get a counted result a set of tool buttons gets enabled in the main tool bar Those buttons allow you to interact with the image to correct the count by any of the following act
20. ation You Il be asked to confirm that the current operation should be canceled Click Yes as far as the count results for that plate are not to be saved by now 3 1 7 Setting up More Operations You can repeat the steps above to get different operation settings adapted to different kinds of colony plates Each operation settings must be given a unique name but the same icon may be used on different operation settings This way you can keep set of operation settings under each button The button will remember the last called operation in the group To call another one use the drop list clicking in the small arrow at right of the button 27 3 2 Colony Counting Operation Run 3 2 1 Select the Operation You Want Select the Operation adequate for your plates from the Operations Tool Bar below the working area If you are not sure don t bother you can change it later The pilot in the Flash amp will stop flashing indicating it s on line and the Operation Run Dialog will open If any of the values shown in the Operation Dialog is not adequate for your plates you may fill it as needed Note that by default the Sample Identifier field will get incremented at each new measure or left blank in case that barcode reader is active The rest of fields will keep their last values 3 2 2 Process Your Plate Place the plate in the Flash amp platform and push the white button there You ll get the processed image of th
21. ation images without saving them systematically or without the need to accept the results of that operation while the operation is alive To do so after running the operation but before accepting or canceling e Inthe File Menu select Export Processed Image or Export Captured Image e Inthe Save Image Dialog select the folder when you want the image saved give it a name and click OK 22 Part 3 Counting Colonies 23 3 1 Create the Colony Count Operation Settings The New Operation button is the left most in the Main Tool Bar If that button is the New Colony Count Operation left click on it If not open the drop list by clicking the small arrow aside the button and select Colony Count The button will remember your last selection The dialog that appears at the left side of the working area is the Edition Dialog for colony count operations The dialog starts at their Image Capture page showing the controls related to image capturing Below the dialog a tool bar allows for normal actions during the edition change page save or restore and get context related help Each page in the dialog will be a step in the process of optimizing the new operation settings Hints e You can save your settings any time by clicking on the Save Changes button and giving an appropriate name or restore the initial or the last saved settings by clicking on the Undo Changes button
22. aware of it In this case o Inthe Settings menu select Environment o In the Environment Settings Dialog set the Barcode Reader settings according to your device o Close the dialog clicking on the OK button o Inthe Main Tool Bar click the Barcode button to get it pushed Plate Identifier Individual plates must also be identified before processing both for filing the results and when using a Work Sheet to get the Operation Settings corresponding to each plate As for the Rack Identifier you have two options Barcode or Auto Increment lt starting in this case from a keyboard entered value Note Plate barcodes are automatically read by the Plate Handler The labels with the barcode must be placed in the lateral wall of the plate in the area below the plate lid If the Handler can t read a plate barcode at normal speed the Handler will make several tries moving the plate slower If it does not succeed the handler will stop after dropping the plate in the Flash amp platform and a dialog asking to enter the 47 Plate Identifier by hand will show in the Flash amp Grow window You can type the identifier or try with a hand reader if you have it installed in the computer Plate Operation Before processing a rack of plates you must specify the operation settings you want applied to those plates That can be done in a plate per plate basis using a Work Sh
23. ay be out of the rack after losing track of their position After you select a Recover Handler you will be asked to make sure a rack with an empty column facing the Handler is waiting for the recovered plates If you click OK in that dialog the Handler starts a sequence of movements oriented to recover any plates what ever they may be and place them back in the rack Such a maneuver may be necessary to recover after a power failure or a plate tangling when a normal Handler Home doesn t work 50 6 3 Handler Work Sheets 6 3 1 Automatic Selection of the Plate Operation When barcodes are read in the plates the operation applied to each plate may be defined by their barcode In this case a Work Sheet table specifies the operation for each barcode Work Sheets are specially useful when they are automatically generated by your Laboratory Information Management system In this case they must be imported from the Flash and Grow as XML or CSV formatted files Work Sheets may also be edited or created manually by using the Flash and Grow utilities Next section explains this point 6 3 2 Work Sheet Edition To edit or create a Work Sheet e If the Flash amp Grow is not in Handler mode click on the Plate Handler Mode button in the main tool bar e Click on the Edit button the pencil witch will be now identified as Edit Work Sheets The Handle panel contents will switch to the Work Sheet Editor
24. ber the device is attached e In that dialog you can also change the folder and format that will be used to save the plate images and if you are going to use an RS232 bar code reader specify the appropriate settings e The Protected Mode option is explained in the next section e Close the dialog clicking on the OK button 1 4 2 Protecting your Settings from Unwanted Changes To protect your settings from unwanted or malicious changes you can run the application in Protected Mode Running in Protected Mode the Flash amp Grow allows all the routine work using the preselected operations but doesn t allow creating editing or customizing any of them Setting the application in protected or getting it back to normal mode is an option you can select in the Environment Settings Dialog While in protected mode the Environment Settings Dialog will be itself protected by a password key that prevents any unauthorized users to get back to unprotected mode To set the application in protected mode e In the Flash amp Grow main menu open Settings Environment Dialog e In the Options section of the dialog set the Protected Mode field to true e Close the dialog by clicking on the OK button To set or change the password key protecting the Environment Settings e In the main menu click Settings Environment If the application runs in Protected Mode the password dialog will open 12 Enter the current password nothing i
25. dd already defined Operation Settings to the toolbar e In the Main Toolbar click on the Operations Folder button to open the Operation Folder Panel e Click and drag the Operation you want added to the tool bar from the Operation Folder Panel to the Operations Toolbar If a button with the same icon exists the moved Operation Settings will be added to that button list if not a new button will be created 40 5 2 Customize the Operation Settings When editing or creating an Operation Settings you set only a part of the parameters that control the Operation execution the rest of these parameters keep default values that are adequate for most purposes but that can be changed if needed Changing the colors of graphic items or the format of results tables are examples of customization already suggested in the previous sections To open the Customization Dialog you must first open the Operation Settings and then click on the Customize Operation button in the main tool bar The Customization Dialog presents the Operation Parameters organized in pages according to their function and grouped in categories according to their scope According to their functions parameters are classed as Plate Image Process Drawing or Options According to their scope parameters may be General Setting Group Setting General Input Group Input or Operation Specific 5 2 1 Changing Setting Values Each time you select a parameter in th
26. e Data Panel is shown below the Image Panel The box at left side of the Data panel shows the existing tables selecting one of them 1ts contents is shown in the panel Note that when an Operation is open and the results table for that Operation exist 1t gets automatically selected in the Data panel 2 3 2 Review Saved Images The Captured and Processed images can be saved for each Operation and recalled from the results table By default plates and halos operations save both images and thereafter you will find the Captured Image and Processed Image columns in the results tables where are saved the image names for each Operation Run If you don t want those images saved modify the results table as explained in Part 5 of this manual to remove the columns corresponding to the unwanted images Images will be named as the Sample Identifier of the operation run followed by underscore and Captured or underscore and Processed and an index number that will get automatically incremented if an image with the same name already exists When you select a row in a results table containing images the images from the selected row are automatically passed to the Image Panel and the Processed Image shown You can switch to the Captured Image by double clicking on the image panel 2 3 3 Reprocess Saved Images As far as the Captured Image has been saved it can be reprocessed with the same or different
27. e Customization Dialog a short text below the dialog explains their function You can edit any parameter value typing in the value field or selecting it from a list or using a specific editor depending on the parameter type When a percent parameters is selected a track bar below the dialog allows a progressive adjust of their value If a plate is being processed pending of results acceptance or cancellation any change in the settings will be immediately applied to the current plate to show the effect it produces on the Processed Image Changing a setting value may affect not only the current operation but the value of that setting may be shared with other operations depending on the Scope or category it has e General Settings have whole application scope and their value can be shared by any operation e Group Settings can be shared by the operations of the same type Halos or Colonies e Specific Settings are not shared but used only by the current Operation e General Input have the same scope as General Settings but their value may be changed in a plate per plate basis e Group Input have the same scope as Group Settings but their value may be changed in a plate per plate basis As explained in the next section the Scope of each parameter can be customized so beware that when you change a General or a Group value the operations that share 41 that value in the same category will use the new value bu
28. eet or by hand selecting the appropriate Operation Settings while the Handler program is stopped The two radio buttons in the Plate Operation box correspond to those two options Note To change the operation settings by hand you can use the Handler Colum Stop or Handler Plate Stop explained below or simply pause the Handler and change the process Handler Stop The Handler Stop box gives different options to have preprogrammed stop points during the rack processing o Rack Handler Stop let s the Handler run till all the plates in rack has been processed o Column Handler Stop makes the Handler stop each time a complete column has been processed o Plate Handler Stop makes the handler stop after a new plate is placed in the Flash amp platform Using those options to stop the Handler program is the recommended procedure to change the Plate Operation Settings by hand during the process Current Target The Current Target fields show the position in the rack of the next plate being processed for fast supervision It specifies the Column in the rack and the Plate Position in that column Plate position count starts at plate 1 in the top of the column Processed Plate Count The Processed Plate Count field keeps track of the total number of plates processed in the rack also for supervision purpose 6 2 2 The Handler Control Buttons The
29. f no password had been used before and click on the Change button Enter the password you want twice and click OK To accede the Environment Settings while in Protected Mode In the main menu click Settings Environment In the password dialog that gets open enter the password and click OK 1 4 3 Centering and Scaling the Image Click on the Image Calibration button in the main tool bar In the left side of the main panel gets open the Calibration Data dialog If the Flash amp device is correctly connected the pilot will stop flashing indicating it s now on line You can change the default name for the table where calibration results are saved and add any commentary text before proceeding Place the centering grid that comes with the instrument in the plate platform of the Flash amp and click their white button You ll get in the working panel the image of the calibrating pattern superimposed with a similar pattern of blue circles Left click near the center of the blue pattern and drag to the center of the captured pattern The image will be re centered and the current X and Y offsets in mm appear in the Calibration Data dialog Left click near the outmost circle in the blue pattern and drag to fit the 80 mm circle in the captured pattern The image will be re scaled and the current Z offset appear in the Calibration Data dialog You can repeat those two steps if centering or scaling is not
30. g the white button in the Flash amp after running an operation is equivalent to successively clicking Accept and Run 2 2 3 2 Trying Different Operation Settings After a run if you are not satisfied with the results you get you can try with different Operation Settings To do so simply select the operation by clicking in the Operations Tool Bar The new operation will be immediately run on that plate and their results shown Clicking on the already selected button will close the Current Operation If there are any results pending of acceptance you ll be asked to confirm that the operation should be canceled before closing 2 2 3 3 Using Drawing Tools After you run an Operation and before results are accepted the results may be interactively improved by using the appropriate set of tools 18 The tool buttons are of course dependent on the type of Operation They appear in the Main Toolbar when you select the Operation Settings and get enabled after each Operation run if interactive process is allowed Interactive processing is allowed by default but it can be disabled in the Customizing Dialog by setting InteractiveProcessing to false 19 2 3 Result Data 2 3 1 Review Results Operations results are saved in tables in the Results Data File To review the saved results you must click on the Results Data File button in the Main Tool Bar While that button is pushed th
31. he Main Tool Bar e Move the mouse cursor to one point in the contour of the circle you want to draw e Push the left mouse button move to make the drawn circle fit the halo you want measured and release button 4 3 3 Drawn an irregularly shaped halo If a halo has been removed or not at all detected but the image allows you guessing how it really should be and it s not circular you can draw the contour of that halo with the mouse and get the equivalent diameter added to the results e Click on the Draw Irregular Halo button in the Main Tool Bar e Move the mouse cursor to one point in the contour of the circle you want to draw e Push the left mouse button move the cursor following the contour of the halo you want measured and release button 4 3 4 Restore a previously removed halo To restore a processed halo previously removed e Click on the Restore Processed Halo button e Move the cursor to the halo you want restored and click 31 Part 5 Customizing the Flash 8 Grow 38 5 1 Customize the Operations Toolbar When you define new Operation Settings the operation buttons are automatically created in the Operations Toolbar and all the Operations Settings get assigned one button Customizing that bar allows you to remove reorder and add buttons and Operation Settings Note Customizing the Operations Toolbar is not allowed while running in protected mode 5 1 1 Unlock and Re Lock the Operations Toolb
32. ic keys You will need it later to activate those options e When you get the key or keys that you need Start again the Flash amp Grow enter the application key in the Flash amp Grow Activation Form and click OK The applications should get open now e If you have any optional keys o Open the About dialog clicking the Help About menu item o Enter the optional keys you have in the appropriate fields in that dialog o Close the dialog o Restart the application 11 1 4 Configuring the Application Environment When running the first time the Flash amp Grow shows a gray panel that will be the work area for the application The menu and the tool bar on top of that panel are the main controls you ll be using in the following steps To identify a particular button we ll use the name that appears as a tool tip when the mouse cursor is placed over that button 1 4 1 Setting the Serial Channel that Controls the Flash amp Device e If you are using the RS232 cable the COM channel you are using depends on the socket you are plugging the instrument It will normally be COM1 or COM2 e If you are using the USB cable a COM channel is dynamically assigned when you install the driver e In the Flash amp Grow main menu open Settings Environment Dialog e In the Plate Imaging Device section of the dialog the drop down list for that field shows the COM channels available in your computer Select the COM num
33. ick and drag on the blue circle to fit it to the inside area of the plate the media surface That is not used by the process but signals the limits of the plate otherwise not visible in the processed image Visualizing the plate size helps having a first sight correct evaluation of the image scale 32 4 1 3 Set the Halos Layer Filter After image capturing click the Next Page button below the dialog to get the Halos Layer Filter page Layer filtering will use the colors and shades in the image to differentiate the best what is inside and what is outside the halos along the halos contours Inside Tones e In the captured image click on a halo near their border and drag to the first of the Inside Tone s box in the dialog A Processed image will appear showing the parts identified as interior of contours colored on semitransparent red e If parts of the contour are not painted you can drag and drop more points from halos contour inside to the same box Outside Tones e If in any parts of the contour the painted area overflows the halo and invades what s background Click a point in that area outside the halos but near their border and drag to the first of the Rejected Tone s boxes The target here is getting the inside of most of the halos contours painted to correctly mark the halos limits Back Compensation e If colors overlap the previous two steps may not be enough to get the halos contour
34. ing a calibration pattern If you have changed or moved the plate don t forget executing a Reset Plate operation from the drop down list in the Handler Run button It s very important making sure the plate doesn t move from the position where the handler lets it Click on the Plate Handler Mode button to exit the Handler mode Click on the Image Calibration button and proceed to run a normal calibration o Click on the Run button to start the process and capture a plate image o Click near the center of the blue pattern and drag to the center of the calibration pattern image o Left click near the outmost circle in the blue pattern and drag to fit the 80 mm circle in the calibration pattern o Click on the Accept button The instrument is now calibrated to the Handler plate position Click on the Plate Handler Mode button to get back to the Handler mode and proceed with as usual to process the rack 52 53
35. ions 3 3 1 Add colonies to the count If any colonies are not being counted because of a severe overlapping or abnormal coloration or any other reason e Click on the Add Colonies button in the Main Tool Bar e Point and click with the Mouse Cursor Cross to the center of the colony that had been not counted You ll see a new cross marks the point and the colony count is incremented e Continue marking other colonies as needed 3 3 2 Remove colonies from the count If any spots in the image are not colonies but get counted as they were e Click on the Remove Colonies button in the Main Tool Bar e Point and click with the Mouse Cursor cross to the cross that doesn t correspond to a real colony to get it removed from the count e Continue for other false colonies if needed 3 3 3 Signal parts of the image not to be counted If parts of the plate are not well counted because bad media surface irregularities or labels or any other artifacts interfering with the count you can remove the whole area out from the count The sample volume will be automatically corrected to discount the not counted parts of the plate and calculate a colonies per ml result based on the correct parts of the image e Click the Remove Area button in the Main Tool Bar e Draw with the mouse cursor the limits of the bad conditioned area while keeping pressed the left mouse button e Continue for other areas if needed 3 3 4 Signal part
36. les You can also restore a previous Work Data File by setting accordingly that file name That s only used in case you run the Automatic Plate Handler WorkFolder That s the folder where the Work Data File is saved and read from ImageFolder and ImageFormat Images are not saved with the other results but in the specified folder either in BMP or JPEG format The results tables keep only the file name of those images Of course as far as images must be saved the current user of the Windows session must have permissions to read and write to the Image Folder 2 3 5 Exporting Data Tables You can export the results data collected by the Flash amp Grow to other applications using csv format common to all spread sheets and database applications The steps to export a table in csv format are the following e Click the Result Data File button in the Main Tool Bar to open the Data Panel e In the Data Panel select the table you want to export e Inthe File Menu select Export Results Data Table e Inthe Data Table Export Dialog select the folder where you want the resulting file give a name to that file and click OK 21 2 3 6 Exporting Operation Images As explained below operation images can be automatically saved by the process each time results are accepted They will be saved in bmp or jpg files and be available in the selected Image Folder You can also save oper
37. lonies from the count sesssesessseesseesseesseesseeesseeesseessersseeeseesseee 29 3 3 3 Signal parts of the image not to be COUNtOdA oooococnnoccccnoccconacccnonncononaconananinnnnno 29 3 3 4 Signal parts of the image to be COUNted ooooocnnncccnoncccnoncnononcnononcnononcconananonnnnnos 29 3 3 5 Signal the only parts in the image to be counted ooooocnococcnocccooacccconacononaninnnnnns 30 Pan ae a ello edo tues 31 Halos Mestre A OS 31 4 1 Create Halos Operation SettiMgS oooococnnococnoncccnnncnonnnanonnnnnononacononcnnnnnnncnnncnnnnnnnnnns 32 4 1 1 Capture Image ni rl cid 32 441 2 See ANG pl ale ame Cel ciori nineye Seo sans nata 32 4 1 3 Setithio Halos EAYGTFUIER sa od da 33 4 1 4 Set the processed image diaMeter ooooconoocccnoncccnonccononanonnncnnonnncnnnncnononocannnccnnnos 34 4 1 5 Shape and Size Filtering is 34 4 1 6 Identify the Operation with Name and Icon ou cece esse aaa aaa aaa aaaawa 34 4 2 Halos Measure Operation Run sica O AS i d 36 A 2 1 Select the Operation You Want scusscdis adnck se ono di GAR 36 42 22 Process Y OUt Plate cc 4 0 isa A A NO da 36 4 3 Improving Your Halos Results Interactively ooonocccnnocccnoncccnoncconancnonancnonananonns 37 4 3 1 Remove a halo that s not correct oooooccnocanocuconacoonnconanonnnonn aaa aan 37 4 3 2 Draw a circular halo woda ao eee do 37 4 3 3 Drawn an irregularly shaped halo oooonnocccnoncccnonccononcnonnncnononccononanonanaconnnos 3
38. ly the outer circles are marked with red crosses Those are the colonies that will get actually counted according to the spiral platting standard e You can yet move the yellow circle in the Processed image if any border effects are yet interfering e Level 1 of Smoothing is normally adequate but in case of very small interfering spots or broken or not circular colonies a higher Smoothing factor may improve the results 26 3 1 6 Identify the Operation with a Name and an Icon and Save When colonies are acceptably marked click the Next Page button to get the Name and Icon page that will serve to identify that operation Set the name and select an icon according to your preferences The Next Page button is now named Run Operation If you click on it and the current operation settings are not saved you will be asked to save the operation Do it now by clicking on the OK button A button with the selected icon and name will appear in the Operations Tool Bar below the working area That s the button you Il use to recall those settings any time you need it The dialog switches to the Pour Plate or Spiral Plate Run Data page That s the dialog with the operation data that can be changes in a plate per plate basis We Il come back to that dialog in the next chapter To unselect the process click on the pushed operation button or simply go ahead with another oper
39. nswer with only a short movement of its articulated parts If that s the case you can conclude that everything is correctly connected and the Handler ready to work If not you ll get an error message indicating that may help fixing the problem 46 6 2 Running the Plate Handler 6 2 1 The Handler Program After you select the Plate Handler Mode from the Main Toolbar you get the Handler Program dialog in the left side of the working area Let s examine that dialog in detail Rack Identifier Each rack of plates must be identified before processing it That will serve for filing purposes and also to identify the correct Work Sheet in case one is being used You have two options to set the Rack Identifier By reading a barcode in the Rack what s the recommended mode or typing it in the keyboard The two radio buttons in the Rack Identifier box correspond to those options If the barcode is not used the value shown by default in that field when a new rack is started will be the last entered plus one A numeric suffix being added if there is no one Note Rack Identifier barcodes are not automatically read by the Plate Handler but will need a barcode reader connected to the host computer If you have a barcode reader that emulates keyboard entry using it is of course transparent to the application If your bar code reader must be connected to a serial channel in the computer the application must be
40. ol cable plug it now to the instrument and to a suitable socket in the PC it s not necessary to shut down the PC nor the instrument for doing so The PC will detect the new hardware and ask for drivers as it did for the camera Say you have the manufacturer disk and direct the installer to the folder named Drivers USBIUL in the Flash amp Grow CD Let the installation continue to its end 10 1 3 Entering the Activation Keys After installing the Flash amp Grow application it must be activated by entering a key number that depends on the host system where it s installed If a IUL representative staff has installed the application for you it should be already activated and you can skip this section If not you must get and enter the activation key for your system Follow the steps below e Start running the Flash amp Grow application from the Start menu or by double clicking its icon in the PC desktop e The Flash amp Grow Activation Form gives you of a System signature that uniquely identifies your system and asks for the Activation key fitting that signature e Note down the signature and close the dialog You must ask a IUL representative providing him the activation key or directly fill and send by e mail or fax to IUL headquarters the form in Appendix 1 of this manual If you have also purchased any software upgrades as Halos Measuring or Plate Handler support don t forget to ask also for their specif
41. on Threshold e The Separation Threshold track bars define the tolerance for color filtering Moving the track cursor nearer to the colony tone makes the filter more restrictive nearer to the background makes it more tolerant Slight changes in these thresholds can help getting the final adjust of the filter Also readjusting the separation thresholds the filter may adapt to plates with slight differences when needed Hints e If colonies or background have different shades but form a continuous of tones try selecting the extreme tones and dropping them to the same colony or background tone box The shades in between the entered tones will be automatically included e On the contrary in case that there are colonies or parts of background of two or more clearly differentiated colors that don t mix in the image use a new box for each color up to four for each category 23 e Colors dropped in a background boxes will be rejected in front of any of the colony tones no matter the box it is The order the boxes are paired will only affect the threshold box colors e As more boxes and more colors are used by the filter the process of the image will take a bit longer so be cautious of not overloading the process with irrelevant colors e You can use the Clear instruction in the context menu of the boxes for clearing a box e The color used to mark colonies as any of the other colors used by the graphic items
42. on of Flash Grow but the diversity of hardware configurations existing in the market makes impossible to have an absolute guaranty specially when other applications run concurrently in the same PC To ensure that you can get the best of the software in any situation superior features are recommended 1 1 2 1 Hardware CPU Pentium4 3 GHz or higher USB Embedded USB2 0 port Intel south bridge ICH4 ICHS and ICH6 are tested and recommended RAM 1024MB ram memory or higher available for the application HD To freely save the high resolution images and results obtained by the software several GB of HD available capability are recommended 1 1 2 2 Software Microsoft Windows Vista or Windows XP with DotNet2 0 installed 1 1 3 Supplied Software The CD distributed with the Flash amp Grow instrument contains the Flash and Grow drivers and software and also support utilities allowing to fit the minimum software requirements from any Windows 2000 or XP system Nevertheless the updating via Internet to ensure language compatibility and last version of the updates should be always preferred 1 2 Software Installation 1 2 1 1 2 2 1 2 3 Installing the Flash amp Grow Application Insert the IUL Flash amp Grow CD in the CD Drive and follow on screen instructions Installing the Camera Driver Connect the Flash amp Grow instrument to the power supply Start running the PC session and then turn the instrument power s
43. pendix 1 of this manual After you have your key follow the instructions given in section 1 3 of this manual for entering additional activation keys in the About dialog 6 1 2 Selecting the Serial Channel that Controls the Plate Handler As explained in the Plate Handler manual the Flash amp device is daisy chained to the Handler thereafter the application needs only one RS232 channel from the host computer to the Handler to control both devices Note With Plate Handler model using RS232 interface is mandatory USB is not supported If your computer doesn t have an available RS232 port you should install a USB RS232 adapter to an USB port in the computer If you are using an USB RS232 adapter a COM channel is dynamically assigned when you install the adapter To know what is the assigned channel follow the steps that follow e Open the Start menu e Right click on MyPC and select Properties in the popup menu e Select the Hardware tab and there click on Device Manager e In the Device Manager open the Ports COM amp LPT node e One of the devices listed here should be the IUL Instruments Flash Control Note down the COM channel indicated in brackets next to the device name That s the channel assigned to your device If you are using a native RS232 port its COM channel usually COM1 or COM2 is assigned by hardware You can know it from your computer manual
44. plates can be integrally done from the Flash amp device without any need to move to the keyboard and mouse in the host computer but in case interactive processing 1s needed On the contrary if you work on the host computer to try different settings or interact with the process you ll prefer commanding the Flash amp from the computer That s done by the Plate Processing buttons in the Main Toolbar 2 2 3 1 Run Accept Cancel Buttons The Run Accept and Cancel buttons in the main tool bar allow a more complete control of Operation execution than the single button in the Flash Their functionality is very straightforward e The Run button starts the current Operation just the same as the button in the Flash amp e After you run an operation the Run button is disabled till you accept or not the current results by clicking on the Accept or Cancel button e The Run button gets also enabled when you interact with the process using any of the drawing tools In this case clicking that button will discard the drawing actions and restore the results of the automatic run e Clicking the Accept button saves the current results adding a row to the selected Results Table and the Operation gets ready to run the next plate e Clicking the Cancel button discards those results and the Operation gets ready to repeat from the beginning or go to another plate Note that pushin
45. r Filter page Here you will get the process adjusted to identify the shade of your colonies in the plate image The color filtering parameters will be automatically set after a collection of sample points you will drag from the image to the filter boxes to instruct the process on what are colonies and what are not Colony Tones e Click on a colony in the Captured image and drag to the first of the Colony Tone s boxes in the dialog The Processed image will appear with the parts with a tone similar to the dragged point colored in yellow those are the parts identified as colonies e If part of the colonies are not yet painted in yellow you can drag and drop more points of the not selected tones to the same box Don t bother if some parts of the background get also painted that should be solved in the next step by defining the rejected colors Rejected Tones e Ifafter the previous step parts of the background are painted as colonies click on these parts and drag to a Rejected Tone s box As far as background tones and colony tones don t overlap the filter will finally paint in yellow all of the colonies and nothing of the background Back Compensation e Jf colors overlap the previous two steps may not be enough to fully isolate the colonies layer Activating the Back Compensation option the process will try to compensate for changes of the background by locally adapting the threshold to it Separati
46. rol Buttons auction 48 6 2 3 Additional Handler Operations cccccesscccssececssececesececssececsscceesseceesseceeseeees 49 6 3 Handler Work Sheets zdac RAA a O GRA R 0 O ARE 51 6 3 1 Automatic Selection of the Plate Operati0N oooooonoccccnnooccconaccnnoncconnnanonanccinnnos 643 2 Work Sheet Edition toos 6 4 Calibrating the Flash amp to Work in the Plate Handler 1 222112211112 Part 1 Setting Up the Application 1 1 Installation Prerequisites The IUL Flash amp Grow instrument runs hosted by a PC that controls its behavior captures and processes the plate images and saves results in file tables The supplied software must be installed in the host PC prior to using the instrument 1 1 1 Minimum Requirements for the Host PC 1 1 1 1 Hardware CPU Pentium4 1 7 GHz or higher USB Embedded USB2 0 port PCI PCMCIA USB2 0 ports are often not compliant RAM 1GB or higher ram memory HD 500 MB free after all the operational system updates are installed 1 1 1 2 Software OS Microsoft Windows 2000 SP4 or XP SP2 or Vista DirectX Version 9 or higher DotNet Version 2 0 or 3 0 Windows Vista comes with DirectX and DotNet natively installed as part of the operating system then no ad ons will be needed to install Flash amp Grow 1 0 Vista systems 1 1 2 Recommended Requirements for the Host PC The minimum requirements stated above should normally be enough to support the normal operati
47. s Activating the Back Compensation option the process will try to compensate for changes of the background by locally adapting the threshold to it Separation Threshold e The Separation Threshold track bars define the tolerance for color filtering Moving the track cursor nearer to the inside tones makes the filter more restrictive nearer to the background makes it more tolerant Moving these thresholds can help getting the final adjust of the filter Also readjusting the separation thresholds the filter may adapt to plates with slight differences when needed Hints e If inside or outside have different shades but form a continuous of tones try selecting the extreme tones and dropping them to the same inside or outside tone box The shades in between the entered tones will be automatically included e On the contrary in case that the halos contour has inside parts or outside parts of two or more clearly differentiated colors that don t mix in the image use a new box for each color up to four for each category e Colors dropped in outside boxes will be rejected in front of any of the inside tones no matter the box it is The order the boxes are paired will only affect the threshold box colors 33 e As more boxes and more colors are used by the filter the process of the image will take a bit longer so be cautious of not overloading the process with irrelevant colors e You can use the Clear ins
48. s of the image to be counted In case you have discarded some parts of the plate and want to recover the count on part of a discarded region e Click the Add Area button in the Main Tool Bar 29 e Draw with the mouse cursor the limits of the area you want recovered while keeping pressed the left mouse button e Continue for other areas if needed 3 3 5 Signal the only parts in the image to be counted You can also signal the only parts of the image you want counted without the need to discard the whole image before e Click the Add Area button after the plate gets processed but before using any other tool to draw or discard colonies Doing so the whole plate gets discarded and only the parts you ll signal will get counted e Draw with the mouse cursor the limits of the area you want counted while keeping pressed the left mouse button e Continue drawing more areas if needed 30 Part 4 Halos Measuring 31 4 1 Create Halos Operation Settings If the left most button in the Main Tool Bar shows the New Halos Measure Operation tip left click that button If not open the drop list from the button and select Halos Measure The button will remember your last selection The dialog that appears at the left side of the working area is the Edition Dialog for Halos Measure operations The dialog starts at their Image Capture page showing the controls related to image capturing Below the dialog
49. t Operations that have that parameter as Specific will not 5 2 2 Changing the Scope of Parameter Values As explained above the Scope of each setting may be customized Let s see an example The Plate Diameter parameter is by default a General Setting After you have adjusted 1t once their value will be the same for any Operation that takes that value from General Settings That s OK in most cases but what happens if we need to process a plate of a different size As far as it is a General Setting we mustn t change the Plate Diameter value in the Edit Dialog or in the Customization Dialog because that will affect all the processes that share that value To have a particular operation adapted to a specific diameter we must first change the Scope of the Plate Diameter in that operation from General to Specific Then we can proceed as usual using editor facilities to set the diameter Now the changes will affect only the current Operation Settings To change the Scope of a parameter e Right click with the mouse in the name of that parameter e Inthe context menu select name Scope and click the category you want for that parameter 5 2 3 Using the Input Dialog There are some settings that the user can change in a plate per plate basis The Sampleld and the Comment are obvious examples in that category and they are already available in the
50. t Table Configuration Dialog that shows the list of columns for that table and the properties of each column Using the controls in that dialog you can edit add remove or change the order of the columns in the table Warning After changing the results table format you must also change the results table name otherwise the Operation will try to add results in the new format to the old table and run into a Table Format Error The Result Table Name can be changed in the Customization Dialog and also in the Run Dialog while the application is not running in Protected Mode 43 Part 6 Using the Plate Handler 44 6 1 Install the Plate Handler with thee Flash amp Grow The assembly of the IUL Plate Handler with the Flash amp device and the Flash amp Grow software running in a host PC composes the perfect solution for automated measurement of large plate quantities To get the IUL Plate Handler Device correctly installed with the Flash amp device follow the instructions given in the Plate Handler manual 6 1 1 Activate the Plate Handler Flash amp Grow to Support the Support for Plate Handler must be activated by a key number depending on your system signature If it has not been activated altogether with primary installation of the software you must get the activation key number by providing your signature to a IUL representative or filling and sending by e mail or fax to IUL headquarters the form in Ap
51. t used as default 15 Clicking a button in the Operations Tool Bar or selecting a name in the drop list associated to a button is the standard way to recall a particular Operation Settings The Operations Toolbar can be customized by adding removing or replacing buttons at will It s intended to give easy access to the currently used Operation Settings Behind the Operations Toolbar the Operations Folder keeps track of all the defined Operation Settings included or not in the Operations Toolbar to allow the recovering of discarded old Operation Settings or maintaining special Operations apart from the button operations The Operations Folder button in the main tool bar gives access to that folder and allows for selecting any defined Operation Settings having or not a visible button in the Operations Tool Bar 16 2 2 Plate Processing 2 2 1 Routine Plate Processing With well conditioned plates the routine work to process a set of plates in the Flash amp Grow is very simple e Select the correct Operation Settings for that kind of plates Then for each plate e Enter the Sample Identifier e Place the plate in the Flash amp platform and push the white button there To enter a sample identifier you can either type it in the keyboard read a bar code or initialize and let go an auto incremented value At each plate run the Processed Image graphically shows the
52. truction in the context menu of the boxes for clearing a box You can customize the color used to mark the halos and any of the other colors used by the graphic items in the image If yellow is not adequate for your plates see part 5 on how to customize the operations 4 1 4 Set the processed image diameter The yellow circle in the Processed image marks the limits of the processed part of the image The processed image will be normally smaller than the media area marked by the blue circle to let out the borders of the plate where the media curvature interferes To adjust the processed image diameter e In the Processed Image click and drag on the yellow circle to let out of the processed area any reflections or artifacts related to the borders of the plate 4 1 5 Shape and Size Filtering Click the Next Page button to get the Shape and Size Filter page The Processed image will show the whole halos as guessed from the contours detected in the previous stage paint in transparent red The haloes that according to the parameters in that dialog can be accepted as valid will include a yellow number that corresponds to their position in the plate e Enter the number of halos that must be in the plate e Select the minimum and maximum diameter of acceptable halos e Level 1 of Smoothing is normally adequate but in case of granulated background or broken halos a higher Smoothing factor may improve the results
53. unctions In the Handler Run list you have the Run Handler Program what does the same as a click on the button and two items more Reinit Handler Program Reinitiating the Handler Program interrupts the current Rack processing and starts a new one When you click that button a warning messages asks for confirmation to prevent the unwanted interruption of the current rack If you click OK in that message the Current Target and Processed Plate Cont are cleared and the Rack Identifier is also cleared or incremented depending on the option selected Reset Current Plate The Reset Current Plate function gets the Current Target plate re dropped in the Flash amp platform It s an important maneuver to ensure the plate is correctly centered in the platform after it has been moved The Flash amp Grow automatically resets the current plate before processing it any time the Handler has stopped with a plate in the platform Calling this function by hand resets the plate without continuing the program That will be necessary any time you want exit the handler mode to process that plate in normal mode A common example of that is running a Calibration Operation as described in the next chapter In the Handler Home button you have only one additional item Recover Handler 49 The Recover Handler is a special maneuver of the Handler to recover plates that m
54. witch on Plug the USB2 0 camera cable the one that comes inseparably with the instrument to a suitable USB2 0 socket in the PC Momentary do not connect the control cable to ensure that the camera is first detected by the PC The camera will be recognized by the operating system as new hardware and a dialog will ask for installing driver software Say you have the manufacturer disk and direct the installer to the folder named Drivers ARTCAM 300MI DRV V 134 in the Flash amp Grow CD Let the installation continue to its end You can verify that the driver is installed by unplugging and plugging again the camera Now it will be recognized by an audible bell sound but should not raise the New hardware detected message If running the Flash amp Grow the application fails to find the camera despite being connected it may be locked to another application or to a previous session of Flash amp Grow Unplugging and plugging again may solve the problem Installing the Control Driver Light and operation control of the instrument is assured independently from video connection through a serial channel that can be either USB or RS232 The instrument will automatically recognize the type of connection that s being used and run accordingly If you will use the RS232 port no drives must be installed You can connect the cable and skip to the Configuring the Application Environment chapter below If you will use the USB contr
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