SynOptics SYNBIOSIS aCOLyte3 User Manual Download Page 50

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Creating a new batch

in the Use External Source for Plate ID dialog box (see

Using an external source for

plate identifiers

, page 42) to display controls for opening the CSV file:

2. Press

to open a standard Windows Open dialog box.

3. Use the Open dialog box to locate and select the required CSV file.

4. Press Open to open the selected file.

5. The contents of the file will be shown in the preview box:

aCOLyte3

User Manual

Summary of Contents for SYNBIOSIS aCOLyte3

Page 1: ...the right to make changes without notice both to this publication and to the product that it describes No part of this publication may be reproduced stored in a retrieval system or transmitted in any...

Page 2: ......

Page 3: ...17 Creating the batch 17 Creating a completely new batch 18 Creating a new batch based on an existing batch or an exported batch file 21 Setting up batches 24 Giving the batch a name 25 The Classifica...

Page 4: ...tions 68 Counting colonies 68 Counting the colonies on a plate automatically 69 Exclude regions 69 Test measurement and adjusting settings 72 Manual colony counting 74 Entering a zero count 75 Closing...

Page 5: ...play properties 94 Managing aCOLyte3 users 95 Windows password security 96 aCOLyte3 user groups 97 Local and Domain Security groups 97 Database location 100 Calibration 101 Camera measurements 101 aCO...

Page 6: ......

Page 7: ...plate if there are any problem areas on an individual plate where colonies cannot be distinguished for some reason the missing area is then automatically allowed for in calculating the total count fo...

Page 8: ...these procedures can also be applied in Measurement mode l Using Measurement Mode to count colonies page 61 which shows you how to count the colonies on a series of plates l Working with results page...

Page 9: ...e before you perform a count Taking measurements Once the batch has been accepted for Measurement mode the process of counting the colonies is very straightforward put a plate in the plate holder pres...

Page 10: ...aCOLyte3 or if you are logged out automatically by aCOLyte3 because you have not used it for a set period of time 5 minutes by default see Logging out and closing aCOLyte3 on the facing page for more...

Page 11: ...box will be displayed Note You may also be logged out automatically and this dialog box displayed if you do not use aCOLyte3 for more than a set period of time 5 minutes by default see System settings...

Page 12: ...Getting started 6 aCOLyte3 User Manual...

Page 13: ...ing the image to a file page 11 l Importing an image from a file page 11 l Calibrating the image page 12 l Viewing batch images page 14 The view batch images procedure is used to view images captured...

Page 14: ...file page 11 l Importing an image from a file page 11 l Viewing batch images page 14 See also l Zooming the image page 10 Loading plates into the instrument To load a sample plate into the instrument...

Page 15: ...ively and the results combined to form a color image this procedure produces more accurate results than can be obtained using a color camera If the image is too light or too dark you can adjust the ex...

Page 16: ...to increase the exposure by small step to increase the exposure by a large step Or Drag the handle in the exposure slider bar Zooming the image By default the image is scaled to fit the image pane in...

Page 17: ...to hold the image l enter a file name for the image 4 Press Save to save the file See also Viewing batch images page 14 for how to export previous images from a batch Importing an image from a file T...

Page 18: ...rated imported image a warning dialog box will be displayed asking if you want to calibrate the image for example Note In order to create an accurate calibration you need to know the actual size of so...

Page 19: ...ine will be drawn back to the starting point for example 4 Click to mark the other end of the feature The calibration edit box and units button will be displayed 5 To change the units a Press the unit...

Page 20: ...e a measurement in Measurement mode the captured image is also saved with the result in the batch To view the batch setup image and images used for measurements 1 Press to display a dialog box The box...

Page 21: ...ng the name of the batch the measurement images will be saved using the plate identifier An xml file containing information about the images will also be saved in the folder 4 To export a single batch...

Page 22: ...Capturing images 16 aCOLyte3 User Manual...

Page 23: ...Configuration tab page 35 for setting up how plate identifiers will be assigned to plates when they are measured l The Measure tab page 47 including l Plate ID page 48 l Dilution page 48 l Setting cou...

Page 24: ...the new batch you will still need to set it up and test it before you can start using it to count colonies see Setting up batches page 24 Creating a completely new batch Note See Creating a new batch...

Page 25: ...cture in Step a ii Press the appropriate radio button to specify whether the plates you are using are circular or rectangular iii For a circular plate enter the Diameter of the plate for a rectangular...

Page 26: ...ill be using iv If you are using a two sector counting frame and the number of colonies counted within the first sector is less than a set threshold the whole frame will be used instead To Set the thr...

Page 27: ...rom scratch To create a new batch based on an existing batch or an exported batch file 1 Press to display the Launch Batch Designer dialog box Go to Step 2 if you want to create a new batch from an ex...

Page 28: ...emplates only to hide any batches in the list that were based on an existing batch or an exported batch file c If there are a large number of existing batches the batch you want to use as a basis for...

Page 29: ...rom Exported Batch dialog box b Press to display the Please select a batch file to import dialog box this is a standard Windows Open dialog box c Use the dialog box to locate and select the required e...

Page 30: ...Discard New Batch button appears near the top left corner of the aCOLyte3 window Press Discard New Batch to abort the new batch you will be asked to confirm that you want to do this l The Accept New B...

Page 31: ...e before you can accept the design see Accepting the batch design page 56 To give a name to a batch Type the name into the Designing Batch box at the bottom of the Batch Designer screen See Setting up...

Page 32: ...the existing batch though you can change them if required If you are creating a completely new batch you will not be able to accept it for taking measurements until you have defined a total plate coun...

Page 33: ...unaffected part This means that you are more likely to want to choose a partial plate frame for an individual plate while you are working in Measurement mode than for all the plates in a batch when yo...

Page 34: ...frame an orange circular drag handle will appear in the center of the frame For example 2 Drag the frame and drop it in the required position Resizing frames Generally frames should be made as large a...

Page 35: ...e to adjust the height drag the left or right side to adjust the width drag a corner if you want the frame to maintain the same shape aspect ratio when you adjust the size Rotating frames You can rota...

Page 36: ...unt button to set simple criteria for detecting and counting the total number of colonies on a plate To set the Total Plate Count criteria 1 Press the Classification tab in the Batch Designer see The...

Page 37: ...te Count controls will be hidden and the icon on the Total Plate Count will show the selected option or c If the button below the image is labeled No Colony Markers press the button and select All Col...

Page 38: ...For example l Split Touching Colonies unchecked l Split Touching Colonies checked c In most cases the automatic sensitivity setting will give excellent results but if the colonies are not being detec...

Page 39: ...the initial counts for plates when you are working in Measurement mode However you will be able to vary these settings for individual plates by carrying out a test count in Measurement mode see Test m...

Page 40: ...play the colony button 2 Press the colony button to display the marker controls 3 Either Select the shape of colony marker you want to use from the marker controls Or a Press Color to display the Stan...

Page 41: ...check box is disabled if there is no barcode reader attached to the PC To display the configuration controls Press the Configuration tab The Configuration tab in the Batch Designer allows you to spec...

Page 42: ...t want to use the same configuration tab settings as in the parent batch Uncheck the Parent Batch check box es for the settings you do not want to use see the references below for how to set independe...

Page 43: ...rom a barcode on the plate to enter identifiers dilutions manually or in combination with a plate list See Using a barcode reader for plate identifiers page 41 for details Manually entered plate ident...

Page 44: ...deselect the external source a Press to display the Use External Source for Plate ID dialog box b Press 4 If Auto increment is selected in the Plate ID box click the check box to deselect it 5 If you...

Page 45: ...on an existing batch there will be a set of Parent Batch controls below the Plate List controls If the parent batch did not use manually entered plate identifiers uncheck the Parent Batch check box es...

Page 46: ...in text to act as a basis for the identifier If the text includes a sequence of digits these will be used as the starting point for the auto incrementing if it includes more than one sequence the righ...

Page 47: ...tifiers on the next page or to input manual identifiers see Manually entered plate identifiers page 64 If you intend to use a barcode reader to read plate identifiers and dilutions where relevant see...

Page 48: ...plate identifiers You can use the following external sources for plate identifiers l a CSV file l a list created in aCOLyte3 To specify an external source for plate identifiers 1 Press to display the...

Page 49: ...ncrementing identifiers or manual identifiers Press When you have selected an external source for plate identifiers the icon in the Plate List box in the Configuration tab will show if you have select...

Page 50: ...e identifiers page 42 to display controls for opening the CSV file 2 Press to open a standard Windows Open dialog box 3 Use the Open dialog box to locate and select the required CSV file 4 Press Open...

Page 51: ...match each plate you are measuring to its identifier dilution in the CSV list see Using a barcode reader for plate identifiers page 41 CSV file format Each line of the file should consist of two strin...

Page 52: ...eans one part sample in ten parts total volume This means that the right hand number must not be smaller than the left hand number 4 Press to add the identifier dilution to the plate list 5 Repeat Ste...

Page 53: ...al batches the dilution control has a different form see Spiral Plate batches page 50 and the Count Restrictions button is hidden To display the measure controls in the Batch Designer Press the Measur...

Page 54: ...igner but it will be ignored when you accept the batch for measurement mode If you have chosen to use an imported plate list or a plate list created in aCOLyte3 the Plate ID control will show Dilution...

Page 55: ...lution boxes to enter the dilution you can type directly into the boxes or use the and buttons to increase or decrease the values Note The left hand box is the sample proportion the right hand box is...

Page 56: ...e current dilution Note The menu contains the dilutions in the current dilution list for the batch 2 Select Edit Dilution List from the menu to open the Dilution List Editor 3 If required to import a...

Page 57: ...itor and add the dilution to the list 5 To change a dilution in the list a Click on the dilution in the list to select it b Press Edit to open the Dilution Editor c Use the dilution boxes to edit the...

Page 58: ...lutions in the list For example No Dilution 1 5 1 in 1000 1 in 10 6 Note aCOLyte3 does not require you to use unique dilutions Setting count restrictions Note The Count Restrictions button is hidden f...

Page 59: ...ry out a test measurement 1 Press the Measure tab to display the measure controls 2 Press Note If you are using an uncalibrated imported image a warning dialog box will be displayed asking you to cali...

Page 60: ...ction you will need to go back to change the batch settings using one of the procedures described earlier in Total Plate Count page 30 If you are happy with the measurement results you can proceed to...

Page 61: ...t is the order they will appear in the Results table To change whether a result will be included in the Results table 1 Click on the result to select it 2 Click on the result again to select deselect...

Page 62: ...to taking measurements Press Notes The button will be disabled until you have carried out all steps required for setting up the batch However even if the button is enabled you will prevented from acc...

Page 63: ...and enter a filename for the exported batch details 4 Press Save to save the batch details file If required you can move the XML file to another PC and use it as the basis for a new batch on that PC...

Page 64: ...recent batches a Type the name or a part of the name of the required batch into the Search criteria box b Press Only batches with names that contain the text you entered will be listed 6 Select the re...

Page 65: ...h You will be asked if you want to delete the image files 9 Press Yes to delete the image files saved with the batch Note Although the batch can no longer be viewed in aCOLyte3 it is not actually remo...

Page 66: ...Creating a new batch 60 aCOLyte3 User Manual...

Page 67: ...or the batch see the following chapter Working with results page 77 9 Close the batch see Closing batches page 75 Steps 2 and 3 are also required when creating and setting up the batch the cross refer...

Page 68: ...ame or a part of the name of the required batch into the Search criteria box b Press Only batches with names that contain the text you entered will be listed 3 Select the required batch in the list 4...

Page 69: ...t mode If required you can adjust the frames settings in Measurement mode by changing the frame type shape size position and orientation for an individual plate before you make a plate measurement You...

Page 70: ...ifier When a batch with auto incrementing plate identifiers is first opened the template identifier set when the batch was created see Selecting auto incrementing plate identifiers page 39 will be set...

Page 71: ...he values Note The left hand box is the sample proportion the right hand box is the total so 1 10 means one part sample in ten parts total volume This means that the right hand number must not be smal...

Page 72: ...e dilution list see Spiral Plate batches page 50 for how to use this dialog box 4 Press the dilution button again and select the required dilution from the Dilution List Note The new dilution list wil...

Page 73: ...urements can be made and an error message will be displayed if you try to perform a count If the plates are not arranged in the same order as the plate list you can choose another identifier dilution...

Page 74: ...n a plate in Measurement mode In most cases you should be able to carry out an automatic colony count by simply pressing a button for details see Counting the colonies on a plate automatically on the...

Page 75: ...automatically Press The results will be added to the Results table see Working with results page 77 for details and shown in the Last Measurement Results panel For a Spiral Plate batch the Last Measu...

Page 76: ...be to choose a Partial Plate frame and or to rotate the frame so that the problem area is not counted To define an exclude region on an image 1 Press to select it Note You may find it helpful to zoom...

Page 77: ...agged out from the first vertex 5 Click to add the new vertex for the exclude region 6 Repeat Steps 4 and 5 as required to place any further vertices until you have placed the penultimate one the incl...

Page 78: ...as many exclude regions as required Test measurement and adjusting settings If required you can carry out a test measurement to check the colony detection for an individual plate without recording the...

Page 79: ...on the image 2 Check the image to make sure that the colonies have been correctly detected 3 If you are satisfied with the colony detection go straight to Step 4 Otherwise if there are problems with...

Page 80: ...unt for a Spiral Plate batch To carry out a manual colony count 1 Press The button will become selected showing that a manual count is in progress 2 Click on the image to count each of the colonies in...

Page 81: ...The image will not be saved with the result even if Save images to file is selected in the Settings dialog box see System settings page 92 See also Zeroing the count page 87 for how to zero a result...

Page 82: ...e are buttons and check boxes for the Other Open Batches in the box below it 2 Either to close a selection of batches a Click in the check boxes for the batches you want to close to select them b Pres...

Page 83: ...ottom of the window for example Note The default choice of which columns are included and their order in the Results table is made when the batch is set up in the Batch Designer but you can change thi...

Page 84: ...dings You can select a row in the Results table by clicking in it and move to the next or previous line by pressing the down or up arrow key on the keyboard To select the next or previous Plate Name i...

Page 85: ...u want to edit by clicking in the plate s result in the Results table see The Results table page 77 2 Press the Edit Result tab to display the Editing Plate panel at the bottom of the aCOLyte3 window...

Page 86: ...The controls on the Edit Result tab and the Editing Plate panel allow you to carry out a wide range of editing operations which are described in the following sections l Editing the plate identifier...

Page 87: ...OLyte3 window 2 Edit the plate identifier in the left hand edit box as required 3 Add to edit the Comments in the right hand edit box as required 4 To edit the dilution where relevant a Press the dilu...

Page 88: ...result see Viewing the audit history of changes on the facing page Undoing and resetting changes To undo all the changes made to a result on the Edit Result tab and the Editing Plate panel see Editing...

Page 89: ...ts table 1 Select the Edit Result tab for the plate result see Editing plate measurements page 78 2 Press to display the Audit History dialog box 3 When you have finished viewing the audit history pre...

Page 90: ...lect the Edit Result tab for the plate result see Editing plate measurements page 78 2 Press 3 Adjust the frame using the same techniques as when you create a batch or before taking a measurement see...

Page 91: ...measurement and adjusting settings page 72 This section shows you how to change the Sensitivity setting for an individual plate after it has been measured To change the detection Sensitivity setting...

Page 92: ...ge 10 4 Save the change to the result see Saving changes to results page 82 Adding exclude regions to a result Note You cannot place exclude regions on Spiral Plate batch results If required you can a...

Page 93: ...ies manually press Clear Markers see Manually adding and removing colonies page 83 If you want to delete a faulty result press Delete Plate see Deleting results page 82 However if you delete a result...

Page 94: ...rt for the current batch l Summary of all Batches to create a summary report covering all the batches in the aCOLyte3 database l Audit trail of all batches to create an audit report covering all the b...

Page 95: ...so that it is not checked Note The Restrict report by batch headings setting has no effect on summary or audit trail reports 4 Press 5 If you chose to create a CSV report a dialog box will be display...

Page 96: ...Working with results 90 aCOLyte3 User Manual...

Page 97: ...page l Changing the color of the frame see Managing aCOLyte3 users page 95 l Setting up user accounts see Managing aCOLyte3 users page 95 l Specifying the location of the aCOLyte3 database on the PC...

Page 98: ...Windows Save As dialog box if you want to save the program version details in a text file 4 Press Close to close the dialog box System settings To view or change the system settings 1 Press the aCOLyt...

Page 99: ...en you carry out a measurement choose Do not save images if you do not want the images saved Note You will only be able to edit results after you have performed a measurement if the image is saved wit...

Page 100: ...can choose l None l Windows l Local User Groups l Network User Groups See Managing aCOLyte3 users on the facing page for full details of what these mean and for how to set up Local and Network User Gr...

Page 101: ...ogram l audit trails will record that changes were made by the user who was logged in to Windows at the time the change was made If you choose None as the Authentication Method there is nothing more t...

Page 102: ...ation Method set to None in the Settings dialog box see System settings page 92 aCOLyte3 uses Windows password authentication to control access This means that in order to log on to aCOLyte3 the user...

Page 103: ...roups Or l Domain Security groups defined across a Windows Server domain If the aCOLyte3 PCs are connected to a network arranged in a Windows Server domain you can use Windows Domain Security groups t...

Page 104: ...dd users to the Acolyte Users group a Right click on the required group in the right hand pane to display a context menu b Choose Add to Group to display the Group Properties dialog box The example sh...

Page 105: ...e user names are valid Windows log on user names if a user name is not found and you entered it correctly you will need to create a new user account with this user name Or i Press Advanced to expand t...

Page 106: ...ion Database location If you are using several aCOLyte3 instruments connected across a network they can share a single aCOLyte3 database In order to do this you will need to specify the location of th...

Page 107: ...rther calibration after delivery However in exceptional circumstances you may need to recalibrate the camera measurements which enable the instrument to measure distances on the image accurately To re...

Page 108: ...Configuring aCOLyte3 102 aCOLyte3 User Manual...

Page 109: ...y splitting 32 33 73 for an individual result 85 86 Comments adding editing 81 82 Company Name 93 Configuration tab 35 47 Count restrictions 52 53 Counting colonies 61 68 75 automatically 69 outline p...

Page 110: ...20 Report compiling 88 89 Resetting changes to results 82 Restrict Results 89 Results 54 55 77 89 adjusting the frame 84 changing order 55 deleting 82 83 editing 78 87 including excluding 55 resetting...

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