Batch Coordinator
Contents
1. Batch Name User Name Input file list Output file list Status column 9 1 Overview In Batch Area the hierarchical structure provides information on current and completed batches To expand the Batch and display Batch specific details click the plus symbol next to Batch Name The selected Batch is expanded displaying the batch name all input and output file names within the batch the name of the user who submitted the batch and status line Click on the minus symbol next to Batch name to collapse the content and only Batch and user names will be displayed Command Sequence of currently selected Batch is displayed in the Command Parameter area Batch Name User Input Output Status Gaussian Bitplane PyramidalCell ir c7 PyramidalCell B Waiting PtK2Cell ims L PtK2Cell BATCH 07 Waiting HeLaCell ims HeLaCell BATCH 07 Waiting New Name Bitplane 9 2 Batch Name In the case when Batch and Command sequence is created using Imaris by default a Batch Name is corresponding to the name of first selected command In the case when Batch and Command sequence is directly created Batch coordinator using Menu File Edit or New Batch button default option for Batch name is New Batch In order to change Batch Name double click on it and enter a new customized name 9 3 User Automatically generated each time when new batch is created by user login session 9 4 Input file Displays the list of all files selected for Batch2. output files names are created in accordance with the rule of output filename Batch Name User Input Output Status amp retina ims 07 retina Rotate Save yyyy mm dd 1 ims c Waiting PyramidalCell ir c7 PyramidalCell Rotate Save yyyy mm dd 1 ims c waiting R18Demo ims 07 R18Demo Rotate Save yyyy mm dd 1 ims 7 Waiting Starting Batch Job To start a Batch job select click on the icon Run a By Running Batch Coordinator the complete command sequence is executing on all input files and Batch processing results are collected and stored in the output file list In status line massage Queued for all file waiting to be executed Batch Name User Input Output Status ES Rotate Bitplane retina ims retina Rotate C7 3 PyramidalCell ir PyramidalCell c7 3 R18Demo ims R18Demo Rot 7 Queued Completed batch job are marked Finished and remain in the batch display Imaris Batch Batch Name User Input Output Status SE Rotate Bitplane retina ims retina Rotate Finished PyramidalCell ir c7 PyramidalCell 7 Finished R18Demo ims 7 R18Demo Rotl Finished Reviewing results To verify results click on the icon next to a Retina output file Imaris as externals applications will be launched processed Retina will be displayed In addition to opening output Batch files directly in Batch Coordinator resulting files can be open in Imaris by selecting and opening Batch file from the file list Open Pyramidall
3. 11 2 Commands Following Commands are available in Batch Coordinator Open ave Flip Rotate Channel Shift Gaussian Filter Median Filter Linear Stretch Gamma Correction Invert ep Bitplane 2008 Normalize Layers Baseline Subtraction Threshold Cutoff Background Subtraction Connective Baseline Display Adjustment Set Coordinates Set Time Points Add Slices Add Channels Add Time Points Delete Slices Delete Channels Delete Time Points Crop 3D Crop Time Resample Time Resample 3D Change Data Type Swap Time and Channels Swap Time and Z Spots Surfaces Matlab Merge Csv Statistics Post Please refer for a more detailed description of the commands and parameters to the Imaris Reference Manual 11 2 1 Open By default set to be a first command in command sequence created either by Batch job Creation in Imaris or directly in Batch Coordinator Expend command line Open by clicking on the plus sign next to command name Command is expended and Parameter File displays current file name in Value column Input file name or directory could be modified either by 1 Entering in the Value column the full path to the new directory along with a new file name or 2 Double clicking open file icon Open File Window will allow selection of new file name or new destination folder To verify and confirm input file double click on the icon x next to file name It open input files with Imaris standard app
4. 3D Reducing the voxel density in a data set but keeping the original relationship between the voxels 11 2 29 Change Data Type Changing data type from current display to 8 16 or 32 bit Imaris Batch 11 2 30 Swap Time and Channels Exchanging the t axis and the channels and re formatting the image 11 2 31 Swap Time and Z Exchanging the t axis and the z axis and re formatting the image that the time dimension is mapped onto the z axis and the z dimension is mapped onto the t axis 11 2 32 Spots Multiple step procedure for automatic detection of point like structures Please refer to the Chapter Spots and Surfaces for Batch command more application details and Imaris Reference Manual for Spots Creation Wizard Command Spots is determining extension and part of the file name of the output files All files with extension IMX and CSV are generated by command Spots regardless of preceding commands in the command sequence The output file name of files with extension IMX and CSV will contain Spots as a command name in the output file name 11 2 33 Surfaces Multiple step procedure for automatic detection and creation of artificial solid objects Please refer to the Chapter Spots and Surfaces for Batch command more application details and Imaris Reference Manual for Spots Creation Wizard Command Surfaces is determining extension and part of the file name of the output files All files with extension IMX and CSV are generated by command S
5. Batch Coordinator It is advisable to start the Batch Coordinator either before or concurrently with the Imaris To open Batch Coordinator double click on the Batch Coordinator icon The software opens with the main screen Supported File Formats Batch Coordinator can read the following file formats i e it can read the image and the parameters Andor Multi TIFF series tif tiff Applied Precision Inc DeltaVision i3d dv Biorad MRC 600 MRC 1024 pic BioVision IPLab Mac ipm Bitplane Imaris 5 5 ims Bitplane Imaris 3 0 ims Bitplane Imaris 2 7 Classic Old ims Bitplane Imaris Scene File imx Carl Zeiss LSM 510 Ism Carl Zeiss LSM 410 LSM 310 tif tiff Carl Zeiss Axiovision zvi Image Cytometry Standard ICS used by Nikon Huygens and others ics ids Leica TCS NT tif tiff Leica LCS lei raw tif tiff Leica series inf info tif tiff Leica Image File Format lif Molecular Devices Metamorph STK series stk MRC primarily electron density volumes as in cryo EM mrec st rec Olympus FluoView TIFF tif tiff Olympus FluoView 1000 OIF oif Olympus FluoView 1000 OIB oib Olympus Cell4R 1 1 standard tif tiff Open Microscopy Environment XML ome Open Microscopy Environment TIF tif tiff Perkin Elmer UltraView tim zpo Scanalytics IPLab ipl TILL Photonics TILLvisION rbi
6. Batch Name Gaussian default option and user name In command parameter window command sequence will contain following commands Open Gaussian Filter Save The same action can be achieved with selecting New Batch command in Menu Eile or Edit Note To initialize a Batch job input files must selected and added 10 2 Delete Batch This option allows deleting selected Batch Select Batch to be deleted The batch will be highlighted in Batch area Click on the Delete Batch Delete Batch button and selected Batch will be removed The same action can be achieved with selecting Delete Batch in the Menu Edit 10 3 Add Files To Add files for Batch processing click on the Add Files Button Choose input files window appears Add Files Select the single file to batch or multiple files with ctrl or shift key All selected files will be added to the Input list and the output files will be generated automatically and added to the Output file list The same action can be achieved with selecting Add Files in Menu Edit To remove input file click on the line to select a file and either press Remove File Button or in Menu Remove Files Edit select option Remove File Note Input files added to the Batch Coordinators have properties defined by acquisition conditions and they affect how files could be processed Bitplane 2008 10 4 Remove Files This option allows deleting selected Files Select Batch and Files to be deleted The
7. Open an image in Imaris 2 Select the first command that will be applied to all images 3 Adjust commands parameters either in Command s window or throughout the Creation Wizard for Spots and Surfaces The effect of the modification and parameter adjusting can be seen instantly in the image as changes are applied 4 Submit the adjusted command to Batch coordinator by click on Add to Batch button add to batch e Add to batch button is available at the bottom of the command window e For Spots and Surface select Tab Creation and Add to batch button is available at the bottom of the Tab Creation 4 panel 5 Repeat process for series of command that you would like to be execute in Batch Coordinator Note Bear in mind that commands are added in Command Sequence into the Batch Coordinator by the order they are entered in Imaris For example if command Flip and Rotate commands were add to the batch the Flip action will be executed first and then the Rotate So before progressing to the next step make sure the batch commands are ordered properly and all parameters are confirmed 6 The last step is selecting command Save as adding the command Save in Batch command sequence 7 Open Batch Coordinator In Batch area a New Batch will be created with automatically created User name and Batch Name A Batch Imaris Batch Name always match the name of the first submitted Imaris command default option In command parameter area the Comma
8. a Batch select command Run The Command sequence will be executed on the all input files The resulting image and statistical files will be collected and saved in the output file list 4 4 Example In this example the compete procedure for setting and executing Batch will be presented You will start with creating the Command sequence containing commands Rotate and Gaussian Filter with adjusted parameters in Imaris Than selection of Input files and the output file list creation will be described followed by description of starting a Batch job The last part will illustrate how the batch resulting files can be reviewed Command Sequence Creation Open Imaris In Menu File select command Open Select image Retina Press Add to Batch button and than open the image Retina A Retina image is displayed in Imaris Main screen Bitplane 2008 Open File Look in ED images a e AE HeLaCell ims rl SwimmingAlgae ims lai PlantCell ims di PtK2Cellims di PyramidalCell ims R18Demo ims BEM File name retina ims Files of type an Files auto format detection xl Cancel Bitplane Imaris 5 5 Reader Configuration I Read only one Time Point Add to batch Resampling Open Menu Image Processing and select command Rotate A Rotate Channels window will appear For Rotation select all channels along Z axis in Counter Clockwise orientation Click on Add to Batch button w SRE submits the command in
9. for creating Batch Commands sequence Spot and Surface In Imaris adjust commands parameters throughout the Creation Wizard 4 Create for Spots and Surfaces The effect of the modification and parameter adjusting can be seen instantly in the image as changes are applied Complete Creation Wizard Select Tab Creation 4 and all parameters values are once more displayed Click on Add to Batch button Add to batch at the bottom of the Tab Creation panel Like other commands Spot or Surface is added in Command sequence and listed in the Command Parameter area Please refer to the Chapter Batch Creation for additional references Note Commands Spots or Surfaces are creating multiple output files from a single input file Two generated output files are Imaris scene with extension IMX and Statistical file with extension CSV for comma separated values Please refer to the Chapter Statistics for additional information about statistical files and Chapter Output File for output file presentation and arrangement Imaris Batch 14 Statistics Files with the CSV comma separated values extension are used to save tabular statistical data and can be opened by the many spreadsheet applications Excel OpenOffice Calc All files with extension CSV are statistical files and generated either by command Spots or Surfaces CSV folder Statistical File Output For each input file new CSV folder is created within batch output folder Ref
10. is selected this function will perform no action 6 7 Preferences The Preferences dialog allows you to customize various settings and to customize Batch environment setting Any changes you make to the Batch Preferences settings take effect in image processing Batch Agent Path The preference option is set in conjunction with Imaris at the time of installation It is advised that only the system administrator has access to it since any change can have serious effect on the system if incorrectly set Browse Click Browse to choose the new directory Number of commands Number of commands will verify altered directory of Batch Agent Path Bitplane 2008 Reload Data Cache limit MB Batch Coordinator uses a data caching mechanism that allows you to process images that are significantly larger than the physical memory RAM installed in the computer system This mechanism writes image data blocks to the disk and reads them back into the physical memory when they are needed Memory Limit MB The value of data cache limit controls the amount of data blocks Batch Coordinator will keep in memory at any time Maximum Number of instances Default setting defined by license type and by default is set to be maximum available number Inserting a smaller number limits the numbers of CPU and permitting use of another applications Batch setting Batch Job path The preference option is set in conjunction with Imaris at t
11. job will be displayed 7 3 Stop When batch is running by selecting Stop in Menu Command an execution of batch process is stopped Current running Batch jobs will be canceled and returned to un executed state In Status column Waiting will be displayed The same action can be achieved with clicking on the Stop button O in Batch Toolbar Stop 7 4 Reset In Menu Command select Reset and finished batch process will be restored to an un executed state This option allows modifying Batch job by inserting new commands in command sequence or new input files The same action can be achieved with selecting Reset button in Batch Toolbar Imaris Batch 8 Menu Help The Menu Help has the following commands User Manual Bitplane AG About Batch Coordinator 8 1 User Manual The User Manual provides you with the basic information about Batch Coordinator The menu s the different Batch Coordinator views and all adjustable parameters in the program To find a specific parameter use the Search function in the online version of the User Manual 8 2 Bitplane AG If your computer is connected to the Internet Batch Coordinator can directly open the Bitplane AG homepage www bitplane com 8 3 About Batch Coordinator About Batch Coordinator Batch Coordinator BITPLANE SCIENTIFIC SOLUTIONS Bitplane 2008 9 Batch Area Batch area summarize all information related to Batch jobs It contains following columns
12. processing To verify and confirm input file selections double click on the icon p next to file name It open input files with Imaris or standard application in a new window To remove file from the input file list click on the line to select file and either press Remove File b button Remove Files or in Edit Menu select option Remove File Advance users option Input files column could be also modified in Command Area Expend command line Open by clicking on the Imaris Batch plus symbol next to command name Command is expended and Parameter File displays current file name in Value column Input file name or directory could be changed either by 1 Entering in the Value column the full path to the new directory along with a new file name or 2 Double clicking open file icon Open File Window will allow selection of new file name or new destination folder Please refer to the Chapter Commands Open for additional information about input files 9 5 Output File The Batch Coordinator can generate a variety of different output files and therefore rule must be adopted to prevent output file names from colliding Secondly in the Batch Coordinator the organization of creating output file names differ These two issues have combined resulted in the sophisticated but straightforward method in which Batch Coordinator handles the output file names creation Output file column Displays the list of all pending or created files as
13. system requirements and licensing options Chapter 3 Display Main screen and gives an overall look of the major areas and toolbars Chapter 4 Provides details of Batch job creation It consider the principles in Command sequence design with an explanation and benefits of creating Command sequence using Imaris An example with screenshots describing a procedure of creating Command sequence and executing a Batch job is also included in this chapter Chapter 5 Describes Menu File Examines techniques for saving and implementing Command sequences and considers options allowing the submission and the execution of a Batch job on different machines Chapter 6 Contain information about Menu Edit and describes creation deletion of Batch and addition removal of batch Files Chapter 7 Gives an overall look of Menu Control and explain how a Batch job can be executed Chapter 8 Describes Menu Help and presents commands that display documentation or other information about the Batch Coordinator Chapter 9 Describes in details Batch Area and summarize Batch jobs specific elements Chapter 10 Discuss frequently used commands presented in Batch Control Toolbars Chapter 11 Describes Command Parameter area Defines all commands recognized by Batch Coordinator It provides guidance for parameter values modifications and emphasizes importance of incorporating the correct parameter values Chapter 12 Discusses control shortcuts of Command Parameter To
14. Batch Coordinator V 1 0 User Manual Ce D TIFIC SOLUTI 1 Introduction Batch Coordinator is an easy to use software designed specially for effective image processing and analyses It simplifies and automates image processing and analysis by executing the specified and customized commands on each image within a multiple image data set By applying the specific command sequence to large numbers of images Batch Coordinator allows benefits of e Significantly reducing multiple image analysis and processing time e Increasing reproducibility of repetitive procedures by decreasing risk of inconsistency e Facilitating comparison and evaluation of multiple data sets by standardized output e Improving and optimizing overall system utilizations by reducing resource consumption e Increasing system flexibility and reusability by decoupling the software components Bitplane 2008 1 1 Preface Information in this book is subject to change without notice and does not represent a commitment on the part of Bitplane AG Bitplane AG is not liable for errors contained in this book or for incidental or consequential damages in connection with the use of this software This document contains proprietary information protected by copyright No part of this document may be reproduced translated or transmitted without the expressed written permission of Bitplane AG Zurich Switzerland For further questions or suggestions please visit o
15. Batch and the possibility of reusing standardized and complex Commands Sequences therefore saving time and increasing reproducibility of data processing Select option in File Menu Save command sequence This will open the Save command sequence window Select the directory and enter the name for the command sequence to be saved or confirm the suggestion Click Save Command sequence is saved and available to be later used in creating New Batch process The default command sequence extension is bex 5 4 Import Batch This option allow to rerun the same Batch or to import data from outside your Batch Coordinator system Select Import Batch in Menu File An import Batch window will appear Click Open or double click on the Imaris Batch select Batch from the list A new Batch job is containing command sequence with the input and output file list added to Batch area The default Batch file extension for is bjx 5 5 Export Batch Export Batch allows Batch to be saved and letter executed exchanged with another Batch user or mailed for a question for the support team Select the Batch you would like to Export Select Export Batch in Menu File and the Export Batch window will be open Select the directory and enter the name for the Batch to be exported or confirm the suggestion and then click Save The default Batch file extension for is bjx 5 6 Exit Terminates Batch Coordinator Note Batch Coordinator saves automatically curre
16. Cel BATCH year month day ims and the Pyramidal cell image is displayed in the viewing area after the batch processing Bitplane 2008 5 Menu File The Menu File has the following commands and shortcuts New Batch Ctri N or Cmd N New Batch from command Sequence Ctrl O or Cmd O Save command sequence Ctri S or Cmd S Import Batch Export Batch Exit Ctri Q or Cmd Q 5 1 New Batch Open the File Menu and then click on the New Batch Batch structure will be created in Batch area with automatically created Batch Name and user name In command parameter window command sequence will contain following commands Open Save The same action can be achieved with selecting Newsatch New Batch button in the Toolbar Note To initialize a Batch job input files must selected and added 5 2 New Batch from Command Sequence To set up a new Batch on an existing Command Sequence select New Batch from command Sequence in Menu File The window Open command sequence will appear Select a command sequence from the list and click Open or double click on the requested file entry Creates a new Batch structure in Batch area based on command Sequence already saved Please refer to the Chapter Commands for more information about organization and modification of Commands Sequence 5 3 Save Command Sequence Save command sequence saves a current command sequence with set of parameter values It provides the advantage of a faster creating new
17. Sequence and commands parameters with specific Values are displayed Command Toolbar The Controls toolbars let you add or delete commands or edit command sequence arrangement by moving selected commands up and down Bitplane 2008 4 Batch Creation Batch consist of Command Sequence applied to selected input files as a singe command unit and the results output files collected in a newly created image file or statistical files Command sequence contain the commands with the specified parameters values command describes the operation you want execute on an input dataset and specifications that a command uses to perform its action are called parameters Batch Coordinator offers a variety of available commands for Batch processing some most frequently used ones for image processing Gaussian filter Threshold adjustment and some more complex like Surface and Spot detection A Command sequence can be created either using Imaris or directly in Batch Coordinator 41 Creating a Batch Command Sequence in Imaris From Imaris commands with Add to Batch button 9 Add to batch can be submitted for Batch processing Imaris command that can be submitted to Batch are in Menu Image Processing and Menu Edit For Commands Surfaces and Spots Creation Wizard must be used for selecting and adjusting parameters and for submitting Tab Creation 4 Using following procedure Command sequence is set up in Imaris and submitted to Batch Coordinator 1
18. Statistics Post by clicking on the symbol Two parameters are available InputFiles and OutputFiles Command Parameter value H Open Spots B Merge Csy Statistics Post InputFiles Post Automatically compiled Bitplane 2008 A value for Input files is automatically generated from individual statistical files A value for the merged Output folder name must be created Click on the open file icon and a new window will be open Specify the folder name for merged Statistical CSV file and save it Alternatively the new directory and a new file name can be entered directly in the parameter OutputFile Value line File name R18Demo Statistic Csv 7 Save as type All Files v Cancel Statistical CSV file name and directory will be written as a value of parameter OutputFile Command Parameter Value H Open Spots B Merge Csv Statistics Post InputFiles Post Automatically compiled Command merge will identify and retrieve from the individual CSV folders all files with the same specific file name all files that share a common statistical variable the same statistical variable and merged in one common file As a result a new merged file will be created containing combined specific statistical variables The names of new merged files will correspond to names of statistical variables from individual files The resulting merged folder will have the same number of statistical files as the numbe
19. a result of Batch processing To view and re examine the changes in output file double click on the icon fx next to file name It open output files by launching external application in a new window 9 5 1 Output File Names In Output column file names and directory are automatically generated in accordance with the rule of output filename Output Files Directory All output files will be placed in the same directory as the input file in the new folder called batch output Output File Names The Output file names generated by using a naming rule comprised of the following By default the output file name is automatically generated from input file name using suffixes batch name command name date stamp and file number The output files inherit the input file name as a fist part of output file name The next part in output file name will be replaced by the Batch Name Please refer to the Chapter Batch Area Batch Name for complete details on setting Batch name The next part of the output file name is command name Only commands linked with the generating output files can appear as a command name Therefore only commands Save Spots or Surfaces which generate output files can appear as a command name in the output file name Please refer below to Output file types and formats for more details The output file name is determined by date stamp the year yyyy month mm and day dd of the files added in the Batch in format yyyy mm dd and num
20. ault_ext gt Select option Default Output Name and you can save output file in the directory you specify All Output filename will be changed according to the rule user has selected Note Both forward and backward slashes can be used and be mixed in the same filename without problems Jobs file name The preference option is set in conjunction with Imaris at the time of installation It is advised that only the system administrator has access to it since any change can have serious effect on the system if incorrectly set Browse Click Browse to choose the new directory OK button To confirm any changes in Preference setting press OK button Cancel If you make changes but decide not to use them click Cancel Bitplane 2008 7 Menu Control The Menu Edit has the following commands and shortcuts Run Ctri R or Cmd R Pause Ctri U or Cmd U Stop Ctrl T or Cmd T Reset Ctrl D or Cmd D The Control commands will be performed on selected entry either files or entire Batch job 7 1 Run Start an execution of batch process by selecting command Run from Command Menu A Command sequence will be executed on all of the input data set files The same action can be achieved with selecting Run Button in Batch Toolbar 7 2 Pause Pause a batch process by selecting Pause command in Menu Command When batch is running it can be paused by selecting the Pause command In Status column Paused with percentage of finished
21. ber of the output files crated User can change value of this column by changing the rule in Menu Edit Preference or edit items one by one Bitplane 2008 in Command Parameter Area Output file types and formats Output file types and formats depend on the commands specified to be executed in Batch job Formats the output files are 1 Images with extension IMS for Imaris files 2 Images with extension IMX for Imaris Scene 3 Statistical files with the extension CSV for data presented as comma separated values All files with extension IMS are generated by command Save regardless of preceding commands in the command sequence The output file name of files with extension ims will contain Save as a command name in the output file name All files with extension IMX and CSV are generated either by command Spots or Surfaces regardless of preceding commands in the command sequence The output file name of files with extension IMX and CSV will contain Spots or Surfaces as a command name in the output file name All files with extension CSV are statistical files and generated either by command Spots or Surfaces Advance users option Files in Output column could be also modified in Command Area Expend command line Save by clicking on the plus sign next to command name Command is expended and Parameter File displays current file name in Value column Output file name or directory could be changed either by 1 Entering in the Value colum
22. efining output name and directory The same action can be achieved with selecting Add Files button in the Toolbar Add Files To modify the input file files list click on the line to select file and either press Remove File Button or in Edit Menu select option Remove File Note Input files added to the Batch Coordinators have properties defined by acquisition These image properties effect how files could be processed Imaris Batch Batch Coordinator E DEAR Fie Edit Control Help 2s oog New Batch Delete Batch AddFiles Remove Files Run Stop Reset Bitplane Batch Name User Input Output Status Gaussian Bitplane PyramidalCell ir 7 PyramidalCell B amp 7 Waiting Waiting Croplimitsmin Croplimitsmax e Se Command Parameter Value Load DataSet File PLK2Cell BATCH 2008 10 15 ims ee Reader All Formats Timereader 1 4 Gaussian Filter H Save DataSet 6 4 Remove Files This option allows deleting selected Files Select Batch and within Files to be deleted The files will be highlighted in Batch area In Edit Menu select option Delete Files Selected files will be removed from Input and Output columns The same action can be achieved with selecting Remove Files Button from Batch Toolbar Remove Files 6 5 Select All The Select All command will create a new selection that includes all Batch in Batch Area 6 6 Select None Select None cancels all selections If nothing
23. er to the Chapter Output files for rule for generating output files name and directory The folder will contain all statistical files created after executing Batch job one for each individual statistical variable Hence Batch job containing the commands Spots or Surfaces even for a single input file will produce the multiple output files As a consequence a large number of statistical files must be processed and analyzed Batch Coordinator provides option for combining multiple CSV statistical files A merger of CS V files is facilitated by the uniform structure within the individual statistical report folders and standardized files naming All file names with matching names of statistical variables area volume intensity are fused together Command Merge Csv Statistics Post To merge CSV Output files of all jobs within a Batch a new command must be inserted into a Command Sequence In Command Parameter Tool bar click on the Add command Button A new command Open appears to be very last command in the Command Sequence Double click on added command line and an arrow appears indicating a drop down window From a list of commands select a command Merge Csv Statistics Post Command Parameter H Open H Merge Csy Statistics Post Command merge will combine datasets with a common statistical variable and incorporate them in one common file containing the specific variable of all input files Expand command Merge Csv
24. files will be highlighted in Batch area Click on the Remove Files button Selected files will be removed from the Input and the Output file list Remove Files The same action can be achieved with selecting option Remove Files in Edit Menu 10 5 Run Start an execution of batch process Click on the Run Button and a Command sequence will be executed on all of the input data set files The same action can be achieved with selecting Run from Menu Command 10 6 Stop When batch is running by clicking on Stop button O an execution of batch process is stopped Current Stop running Batch jobs will be canceled and returned to un executed state In Status column Waiting will be displayed The same action can be achieved with selecting Stop from Menu Command 10 7 Reset Click on the Reset button and finished batch process will be restored to an un executed state This option allows modifying Batch job by inserting new commands in command sequence or new input files The same action can be achieved with selecting Reset in Menu Command Imaris Batch 11 Command Parameter Area This chapter describes all commands that are recognized by Batch Coordinator Commands could be defined as a set of actions executed on each file in the input file list Information and specifications that a command uses to perform its action are called parameters In simple terms the command is what is done the parameter is how it does it All co
25. he time of installation It is advised that only the system administrator has access to it since any change can have serious effect on the system if incorrectly set Browse Click Browse to choose the new directory Coordinator path The preference option is set in conjunction with Imaris at the time of installation It is advised that only the system administrator has access to it since any change can have serious effect on the system if incorrectly set Browse Click Browse to choose the new directory Remote address installation The preference option is set in conjunction with Imaris at the time of installation It is advised that only the system administrator has access to it since any change can have serious effect on the system if incorrectly set Default output name This preference can be adapted and changed by all users Preferences allow you to define default directory of output files as well default output file name The default location is the input file directory In a input file Imaris Batch directory a new folder is created with the name is batch output The default output file name is created by input file name with addition of Batch and command name date stamp and file number The output file extension is predetermined by the type of batch file being created lt source_path gt batch output lt source_name gt lt batch_name gt lt command_name gt lt year gt lt month gt lt day gt lt fi le_no gt lt def
26. lication in a new window 11 2 2 Save In order to save output file from Batch job it is necessary to include Save as a last command in command sequence Command Save is determining extension and part of the file name of the output files All files with extension IMS are generated by command Save regardless of preceding commands in the command sequence The output file name of files with extension IMS will contain Save as a command name in the output file name Expend command line Save by clicking on the plus sign next to command name Command is expended and Parameter File displays current file name in Value column Output file name or directory could be changed either by Imaris Batch 1 Entering in the Value column the full path to the new directory along with a new file name or 2 Double clicking open file icon Open File Window will allow selection of new file name or new destination folder To verify and confirm output file double click on the icon 4 next to file name It open output files with Imaris standard application in a new window 11 2 3 Flip Flip image channels either as a group or individual channels in x y z direction 11 2 4 Rotate Rotates image channels either as a group or separately in Counter Clockwise Clockwise orientation 11 2 5 Channel Shift Allows moving channels relative to one another 11 2 6 Gaussian filter The Gaussian filter smoothes the image The filter value can be applied separately t
27. mmands supported by Batch Coordinator are closely associated with commands in Imaris 11 1 Overview In the Command Parameter Area a Command Sequence of selected Batch is displayed A full list of the commands is accessible by double clicking on the command line Double click on the command line and an arrow appears indicating a drop down window with a list of all Batch Coordinator available commands names In Commands Parameter Area the hierarchical structure of Command Sequence provides information on currently selected command To expand the Command sequence click the symbol next to Command Name The selected command line is expanded displaying the all the parameters values specific for selected command Click on the symbol next to Command name to collapse the content and only Command name is shown To change order of Commands in sequence the Up and Down buttons of Command Parameter Toolbars can be used When command is expanded double click on the Value column in parameter line to fine tune the values within the command Note For each command in the Parameters collection a Value must be set from a specific list of choices Please refer to the Chapter Values for possibilities and risks of modifying command values Command Parameter Value 5 Load DataSet File PyramidalCell ims ye Reader All Formats Timereader 1 Croplimitsmin Croplimitsmax Resample 4 Gaussian Filter Load DataSet
28. n the full path to the new directory along with a new file name or 2 Double clicking open file icon Open File Window will allow selection of new file name or new destination folder Multiple output files statistical files and Imaris scene can be created by selecting commands Spots or Surfaces Please refer to the Chapter Statistics for additional information about statistical files presentation and Chapter Commands Save for output file presentation and arrangement 9 6 Status The Status line displays and reports the full status messages on any batch For unprocessed files in Status line message is Waiting After starting a batch job percentage of execution is displayed with bars indicate the amount of progress When the progress bar reaches 100 percent file has been successfully processed all commands executed and output file saved in the designated folder Completed batch job are marked Finished and remain in the batch display Unsuccessful batch and job items are marked Crashed and remain in the batch display In status line massage Queued for all file waiting to be executed Imaris Batch 10 Batch Control Toolbars Batch Control Toolbars has following buttons New Batch Delete Batch cette sateh Add Files adries Remove Files remove ries Run rm Sto p so Re S et Reset 10 1 New Batch Click on the New Batch icon Batch structure will be created in Batch area with automatically created New Batch
29. nd Sequence will contain the list of Imaris selected commands following command Open The last command in the Command Sequence should be command Save 4 2 Creating a Batch Command Sequence in Batch Coordinator Batch job can be created alternatively in Batch coordinator rather than selecting commands from Imaris Select command New Batch from Menu File or press New Batch button and default command New Batch sequence is created In command parameter window command sequence will contain following commands Open Save To modify the commands of New Batch double click on the command line An arrow appears indicating a drop down window From a list of commands select a new command The command sequence is changed in accordance with a selection Note In contrast to the command sequence creation by Imaris creating a command sequence directly by Batch Coordinator sets parameters at default values As a result parameters will not be adjusted and optimized to fit the Batch process and analysis specific requirements Therefore it is highly advisable to create Batch job with command sequence and adjusted parameters using Imaris Please refer to the Chapter Values for additional reference 4 3 Batch job To complete Batch job input files must be added by clicking on the button Add Input files All selected files will be added to the Input file list and the Output files will be generated automatically and added to the Output file list To initialize
30. nd an upper threshold values It applies these thresholds to divide the image into regions and then processes each region with a Baseline Subtraction using either the lower or the upper threshold The threshold values can be applied separately to any of channels or to all of them 11 2 16 Display Adjustment The Display Adjustment manages channel visibility controls opacity and limits color contrast range 11 2 17 Set Coordinates Defines image coordinates 11 2 18 Set Time Point Manages file time stamp modification and last accessed time 11 2 19 Add Slices Adding image slices Data sets must correspond in image dimension channels and time points 11 2 20 Add Channels Adding channels extend or complete the data set information Data sets must correspond in image dimension channels and time points 11 2 21 Add Time points Adding time points to the data set Data sets must correspond in image dimension channels and time points 11 2 22 Delete Slices Deletes slices from data set 11 2 23 Delete Channels Deletes channels from Data set 11 2 24 Delete Time Points Deletes time points from Data set 11 2 25 Crop 3D Cropping unwanted parts of an image reducing data set down to the region of interest 11 2 26 Crop Time Reducing the total number of time points at the beginning or end of the series of images 11 2 27 Resample Time Reducing the total number of time points displaying the images at a faster speed 11 2 28 Resample
31. nf Plus it can read general TIFF series or BMP series Imaris Batch 3 Main Screen The main screen in Batch Coordinator provides the facility to build submit and process batch jobs It has two main areas and two Toolbar buttons sections Batch Area Command Parameter Area Batch Control Toolbar Command Toolbar From this screen all of the batch component can be accessed edit and managed The menu bar at the top of the window contains the entries File Edit Control and Help Each Main screen component is documented in more detail in the following sections ImarisBatchClient File Edit Control Help O Q Batch Control Toolbar New Batch Delete Batch AddFiles Remove Files Run Stop Reset Batch Name User Input Output Status Batch Area Command Toolbar 6 Command Parameter Command Parameter Area Batch area The central area of the screen is Batch area Batch area provides detailed specification of Batch It contains all the information of Batch Batch name with input and output files names user name and Batch status information Batch Control Toolbar Batch Control Toolbar contains shortcut buttons named New Batch Delete Batch Add Files Remove Files Run Stop Reset These shortcuts represent the core tools available to the user The same action can be accessed via the Menu File Edit or Control Command Parameter Area For selected Batch in the Command Parameter area all Commands
32. nt setting Command Sequences and files even after exiting the program Bitplane 2008 6 Menu Edit The Menu Edit has the following commands and shortcuts New Batch Ctrl N or Cmd N Delete Batch Add Files Ctrl M or Cmd M Remove Files Select All Ctri A or Cmd A Select None Preferences Ctrl P or Cmd P 6 1 New Batch Open the Edit Menu and then click on the New Batch Batch structure will be created in Batch area with automatically created Batch Name New Batch and user name In command parameter window command sequence will contain following commands Open Save The same action can be achieved with selecting Newsatch New Batch button in the Toolbar Note To initialize a Batch job input files must selected and added 6 2 Delete Batch This option allows deleting selected Batch Select Batch to be deleted The batch will be highlighted in Batch area In Edit Menu select option Delete Batch Selected Batch will be removed The same action can be achieved with selecting Delete Batch button in the Toolbar 6 3 Add Files To Add files for Batch processing select in Menu Edit and choose Add Files Choose input files window appears Select the single file to batch or multiple files with ctrl or shift key All selected files will be added to the Input list and the output files will be generated automatically and added to the Output file list Refer to the Chapter Preference for changing automatic option for d
33. o any of channels or to all of them 11 2 7 Median Filter The Median Filter replaces the intensity of each voxel with the statistical median of the intensities of neighboring voxels The filter value can be applied separately to any of channels or to all of them 11 2 8 Linear Stretch Linearly extending image contrast to the new limits Minimum and Maximum value can be applied separately to any of channels or to all of them 11 2 9 Gamma Correction Intensifying the gray value of a specific range of voxels 11 2 10 Invert Inverting all channels individually or all together 11 2 11 Normalize Layers Normalize Layers individually or all together 11 2 12 Baseline Subtraction Baseline Subtraction subtracts the baseline value from the intensity of every voxel in the image The value can be applied separately to any of channels or to all of them 11 2 13 Threshold Cutoff Threshold compares the intensity of every voxel in the image to the threshold value The voxel intensity values below are assigned new intensity a threshold value new The Threshold Cutoff values for the channels may differ 11 2 14 Background Subtraction Applies a Gaussian filter to define the background at each voxel and then performs a Baseline Subtraction of this variable background The filter value can be applied separately to any of channels or to all of them Bitplane 2008 11 2 15 Connective Baseline The Connective Baseline works with two a lower a
34. olbars used for managing commands in Command Parameter Area Chapter 13 Provides an explanations of unique features of commands Spots and Surfaces Chapter 14 Describes the output Statistic file It provides a screenshot example of managing statistical files after executing Batch job with commands Spots and Surfaces Imaris Batch 2 Getting Started This chapter describes Installation Licence Starting Batch Coordinator 2 1 Installation The software is delivered on a standard CD or downloaded from www bitplane com The CD includes a folder containing the necessary manuals or the manuals can be downloaded Minimum hardware software requirements are Windows XP Vista or higher Mac OS x10 40 or higher CD ROM Network facilities for image import from the microscope 512 MB RAM gt 1 GB recommended Bitplane also recommends e A database for storing images e g Image Access Installation To install the software please proceed as follows e Insert your Batch Coordinator CD Rom in the computer e Follow the instructions on the screen e The installation is completed automatically 2 2 Licensing Options Batch Coordinator is designed as a high throughput high availability software that targets both individuals as well as large institutes and corporate It provides the confidence of high assurance trustworthy systems in addition to the benefit of low cost software support and maintenance plus guaranteed long term s
35. ommand Parameter Value Open Rotate Gaussian Filter Save To demonstrate the principle of submitting the parameter values from Imaris to Batch coordinator click on the symbol next to the command Gaussian filter On expanded command line all parameter values are available The value for parameter Sigma is set to be 0 2 um as set by Imaris for Filter Width in Gaussian filter window Value for Parameters Channel is on on as filter be applied to both channels Command Parameter Value Open Rotate fe Gaussian Filter Sigma _ annels on on Save Input files The next step in is selecting all files that will be processed with created Command sequence Click on the Bitplane 2008 Add files Button ri and Choose input files winnow appears Choose input file Look in images fa Het acell ims a PlantCell ims My Recent di PtK2Cell ims Documents a j Desktop My Documents My Computer My Network File name tetina ims PyramidalCellims R18Demo ims Places Files of ype Image Fie 7 zl Select files for Batch execution and click on the Open All selected files will be added to the Input list in Batch area Output Files The Output files names and directory will be generated automatically and added to the Output file list All output files will be placed in the same directory as the input file in the new folder called batch output The
36. r of calculated statistical variables If commands spots or surfaces are not present in the Command Sequence Merge Csv Statistics will be ignored Excel files Besides CSV format statistical data can be also created as XLS file Excel files The following steps are used to change format of statistical file Please proceed as follows In Batch area select Batch containing Command Sequence with commands Spots or Surfaces Expand command Spot or Surfaces by clicking on the symbol The type of statistical output files is defined in parameter Statisticswriter and value is set to be by default bpStatisticsWriterCsv Change value of StatisticWriter parameter from bpStatisticsWriterCsv to bpStatisticsWriterExceXls Note Parameter values are case sensitive As a result for every input file an Excel file will be created and saved The statistical variables will be organized in spreadsheets Imaris Batch
37. ssing and analysis requirements Replacing and adjusting variables directly in a batch file could result in Batch job not execute properly as the batch command act in accordance with the parameters entered Because batch process is operating automatically if parameter values are used incorrectly any command can stop the process without necessarily giving the user any indication there is a problem Note Parameter values are case sensitive Imaris Batch 12 Command Parameter Toolbars Bringing users the control of the Command Parameter area Use command toolbars to move up or down commands through a list of commands or to add or delete commands in command sequence Changes can be seen directly in the command list Up Move selected command up in command sequence Down Move selected command down in command sequence Plus Add a new command to existing command sequence A new added command by default is Open Minus S Remove command from command sequence Please refer to the Chapter Commands Value for additional information and advices Bitplane 2008 13 Spots and Surfaces The commands Spots and Surfaces have many similarities to other Batch commands but there are some distinct differences that need to be taken into account when creating Batch job containing the Command sequence with commands Spots or Surfaces Due to Commands complexity it is essential to use Imaris Spots and Surfaces Creation Wizard
38. standardize command sequence performed on each input image within a large data set Generate automatically output file directory and names for each Batch job Pause resume cancel and obtain the status for any submitted batch and or any individual job Manage batch job by add or delete commands and fine tuning parameters values Launch externals applications to inspect input output data files i e Imaris or Excel Runs both on Mac and Windows Command Sequence A command sequence can include following commands Flip rotate invert convert crop Data Set etc Crop resample add delete swap channels and time points etc Change the data type voxel size and time stamps Apply a Gaussian or Median filter Threshold Adjustment by Baseline and Background Subtraction Threshold Cut off Connective Baseline Contrast change by Linear Stretch Gamma Correction Normalize Intensity Display Adjustment Spots and Surfaces analysis with Detection Tracking and Statistics Bitplane 2008 1 3 About this Manual This manual describes all the features of Batch Coordinator This User Manual provides a description of all menu entries display modes functions and parameters The manual is organized into 14 Chapters Chapter 1 Provides an introduction to the Batch Coordinator It describes the function and demonstrates basic capabilities and features of the Batch Coordinator Chapter 2 Describes installation procedure
39. to Batch Coordinator Rotate Channel s Channel 1 Collagenlv TxRed All Channel s Axis Os ely Ole Orientation Counter Clockwise Clockwise Add to batch Open Menu Image Processing and select command Gaussian filter In Gaussian filter window select both channels and enter 0 2um as a Filter Width value Click on the Add to Batch button w cote tea submits the command into Batch Coordinator Channel 1 CollagenI TxRed All Channel s Filter Width 10 200000 um E Add to batch The last step in creating the Command Sequence in Imaris is selecting a commands Save as Click on the Add to batch button and command Save added the command Sequence in Batch Coordinator Imaris Batch Save inc CD images Dr EB Mi HeLaCell ims a SwimmingAlgae ims a Plantcell ims M PtK2Cell ims di PyramidalCell ims R18Demo ims a BEM File name retina ims Save as type Bitplane Imaris 5 5 ims v Cancel Advanced Save Options Format Settings Add to Image ccess database 9 Add to batch Batch Coordinator W Batch Coordinator Open a Batch Coordinator A New Batch with User Name and Batch Name Rotate is automatically created and displayed in Batch area Batch Name User Input Output Status Rotate Bitplane In Command Parameter area the Command Sequence is displayed The command order is the same as commands were selected and submitted in Imaris C
40. upport through participation from a booming Imaris community The Imaris community benefits from frequent updates better portability to different computer systems and the ability to directly contribute through software enhancements and improvements Stand Alone This licensing option allows Batch Coordinator to be placed on Mac or Windows computer system Imaris does not have to be present and this version of Batch Coordinator does not use or depend on the licenses of Imaris Stand alone Batch Coordinator is available in the following configurations Stand Alone up to 2 parallel jobs Stand Alone up to 4 parallel jobs Stand Alone up to 8 parallel jobs Stand Alone up to 16 parallel jobs Bitplane 2008 Stand Alone up to 32 parallel jobs Imaris Dependent This licensing option allows Imaris batch to be placed on Mac or Windows computer system but utilizes licenses of Imaris and its modules as part of its operation For example if you want to perform batch job that require tracking and the output of the statistics from those tracks this version of Batch Coordinator would use the Imaris Imaris MeasurementPro and ImarisTrack licenses The advantage of this option is that it is lower cost than the stand alone version The Imaris dependent version of Batch Coordinator comes in two configurations Imaris dependent up to 2 parallel jobs Imaris dependent up to 4 parallel jobs 2 3 Starting Batch Coordinator Starting
41. ur web site at www bitplane com or contact support bitplane com Bitplane AG Badenerstrasse 682 8048 Zurich Switzerland November 2008 Bitplane AG Zurich All rights reserved Printed in Switzerland Batch Coordinator User Manual V 1 0 Imaris Batch 1 2 Product Overview Batch Coordinator collects commands that you might ordinarily issue in Imaris into a single batch job and execute them together rather than entering each command individually and processing each image separately Batch Coordinator ensures that image analysis and processing is carried out in exactly the same way every time for every single image in a large data set The Batch job has four stages 1 To start Batch processing a command sequence is created in Imaris with adjusted parameter values By default Batch commands will be launched in Batch Coordinator automatically each time they are submitted using Imaris Selecting images for processing and analysis using Batch Coordinator Images are placed in an input file list and added to the Processing Queue Output file names and directory were automatically generated and placed in the output file list Running Batch Coordinator executing the complete command sequence on selected input files and collecting results in the output file list Reviewing the results either in Imaris or in Excel Batch Coordinator Features The Batch Coordinator has following features Customize and
42. urfaces regardless of preceding commands in the command sequence The output file name of files with extension IMX and CSV will contain Surfaces as a command name in the output file name 11 2 34 Matlab Developing and integrating of custom algorithms specifically tailored to scientific applications A variety of function is offered Data set Spot Filament Track Surface Camera Stereology functions Available only for Windows 11 2 35 Merge Cvs Statistics Post Collects all batch statistical files in to one combined file Please refer for a more detailed description of the command to the Chapter Statistics 11 3 Values Batch should be able to be run unattended To obtain correct values for batch processing it is important to ensure that the values are corresponding correctly to the image setting in every regard Therefore it is absolutely critical that values are checked in Imaris Test and verify all command parameter values in the Imaris before placing them in a batch process The simplest method of setting correct variables for a command sequence is to open Imaris and create a New Batch with a selected Imaris Command sequence Please refer to the Chapter Batch Creation for additional references Bitplane 2008 Risks and Cautions Avoid editing batch commands values directly in Batch Coordinator In order for the batch file to work correctly parameters must be set in accordance with image acquisition and exactly fitting proce
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