This panel determines the actions that are performed when an FCS file is read into the program for analysis. There is a tab for each "level" in the batch, so that you can set up different actions for different kinds of files.
Select a tab to view or edit the actions for the associated batch level.
Commands that appear on each tab
Enable
Enable the actions defined on this tab.
Level Name
A name for this level
Description
A description for this level
Initialize and Open
Template
Open a specific GemStone model template.
Open Template Options
Set options for opening the template, including the file name and path. See Properties for File Open and Save for additional details.
Compact File
For FCS files from Fluidigm instruments, this option will re-write the FCS file eliminating extraneous segments from the file. It will have no effect on other FCS file types.
Read File
Read the FCS file associated with this batch item.
Panel Tube Options
Select the option that describes the files on this level of the batch:
Options |
|
One Tube |
This file represents the only tube in the panel. |
First Tube |
This is represents the first tube in a multi-tube panel. |
Subsequent Tube |
This is represents the second or greater tube in a multi-tube panel. |
Analysis
Auto Analyze Data
Initiate the Auto Analysis command after the file is read.
Enrich Data
Initiate the Enrich Data command after the file is read.
Classify File
Initiate the Classify File command after the file is read.
Update Cen-se'
This command updates the Summary map and the Cen-se' plot to display named populations and cell types.
Finish Up
Pause
Enable this option to pause batch processing before printing, saving, and continuing to the next file. When this command is triggered, a dialog is displayed indicating that processing is paused. The dialog shows a count-down timer and will automatically close and continue after the timer runs out. If the user clicks away during the pause, the timer is shut off and the program will wait until the user clicks the Continue button before it advances.
Print Report
Print the report.
Save Document
Save the analysis document after the analysis.
Save Document Options
Set options for saving the document, including the file name and path. See Properties for File Open and Save for additional details.
Save PDFs
Save PDFs for reports.
Save PDF Options
Set options for saving PDFs, including the file name and path. See Properties for File Open and Save for additional details.
Save Graphics
Save graphics for objects that have been selected.
Save Graphic Options
Set options for saving graphics, including the file name and path. See Properties for File Open and Save for additional details.
Save Database
Save the database after each analysis.
Save Database Options
Set options for saving the database, including the file name and path. See Properties for File Open and Save for additional details.
Synthesize Data
Synthesize Data
If enabled, new data values will be synthesized based on the selected options. This option is typically used along with the Export FCS options to create and export synthetic data for experimentation.
Synthesize Data Options
This command displays the Properties for Synthesize Data dialog. This dialog is used to set how much to vary the intensities of populations when synthesizing data. The range of intensities is defined by Low Intensity Factor and High Intensity Factor. A value between these two factors is randomly selected for each synthesis.
Export and Merge FCS
Export FCS
If enabled, an FCS file representing the result of the analysis is exported.
Export FCS Options
Set options for exporting FCS files, including the file name and path.
Merge FCS Option
Choose an option for file merging. File merging allows a set of related files (e.g. a panel of tubes) to be merged into one file containing the union of all parameters in the set. The program synthesizes data for missing parameters.
Merge Options |
|
Don't merge |
Disables file merging. |
Start merge |
Creates a new file to start merging data. |
Add to merge |
Adds to a merge file. This option is only valid after a "Start merge" action and before a "Finish merge" action. |
Finish merge |
Finishes the file merging and closes the output merge file. |
Advanced Options
Stop Auto Advance
Stop the Auto Advance of the batch processor.
Use Custom Actions
Enable Custom Actions mode and the ability to create custom action scripts.
Custom Actions
Edit the actions in the script. This is an advanced feature that provides access to additional scripting commands. See Edit Actions for more information.