Knowledgebase: What are the new Batch Processing run modes and when should I use them?

FCS Express 6 offers three Batch Processing run modes for more versatility and flexibility in your data analysis.

The 3 run modes are:

  • Run
  • Rerun
  • Review

The expandable sections below will provide examples as to when a specific run mode would be used.

Also see our Batch Process Run Modes Application Examples.

I am analyzing a new data set and I would like to have FCS Express export the data in different formats for each sample.

The Run mode will allow the user to perform batch processing as if it was the initial attempt. In other words, batch processing will be performed as if batch processing was never performed for the current data set or layout.

During the running of batch processing, users can select the batch processing option to Unconditionally pause between iterations. This will allow FCS Express to pause as the next data iteration is loading into the plots and gives the users the opportunity to adjust gating as needed for each sample.

FCS Express will automatically record Snapshots for your data when batch processing is Run. If batch processing has been Run and the Run mode is selected again, the original Snapshots will be wiped out and overwritten by the Snapshots taken during the current Run mode.


When to use Run for batch processing:

If performing the initial batch processing run for the data set within the Data List, or to overwrite the original Snapshots that were taken during the initial batch process.

Applications Example: In the example below, we have a layout that contains 3 different 10 color samples that need to be analyzed. We will Run the initial batch process on these samples in the Data List to export data according to the Batch Actions listed in FCS Express. With the option for Unconditionally pause between iterations selected, FCS Express will pause between each sample so that we can adjust the gating strategy during the batch process.

I have performed batch processing on a data set, but I realized that I made a mistake and I need to go back, fix the mistake and export the new and updated results.

The Rerun mode will allow you to perform batch processing and the batch actions that are created and active, but will also apply any Snapshots taken during a previous batch process, or if Iteration Snapshots were taken manually using the blue Previous/Next buttons, found in the Data tab, under the Change Data On All Objects section.

Users can use the Rerun mode in tandem with the conditional Batch Processing Options that are now available in FCS Express. This will allow batch processing to conditionally pause if:

    • a condition is present within the analysis for the current iteration. For example, if a condition is created if there is greater than X% of cells in Gate 1, FCS Express will pause if the % of cells in Gate 1 is greater than X.
    • an iteration is flagged, either from the Data tab or from the batch processing progress window.
    • the users lists specific iteration numbers.

    If one of the conditional options are selected and the batch process is Rerun, FCS Express will automatically apply the snapshot taken during the initial batch process, or, iteration snapshots that were taken manually, but will only pause for the iteration that satisfies the condition according to the batch option selected.


    When to use Rerun for batch processing:

    If data needs to re-analyzed and data needs to re-exported as part of batch processing export products, or, if Iteration Snapshots were applied and your data needs to be exported as defined by the batch processing actions.

    Applications Example: In the example below, we will Rerun our prior batch process for the three 10 color samples contained within the Data List. We can use the same Unconditional Pause that we used in the initial run, or, we can rerun to readjust gates that were previously defined. The new gating positions applied during the Rerun have allowed us to re-analyze our data set quickly and easily.

I have batched my data and have earmarked samples for review prior to exporting my data, or, I need to have my gating strategy reviewed by a supervisor prior to exporting the data.

The Review mode will allow the user to review data, provided that one of the conditional pause options has been selected and the condition has been met. Please note, if no option is selected, the user will be prompted with this message:

Please note that even though batch processing commences, the batch actions will not be performed. Simply, data will be displayed with the appropriate Snapshot applied for the data set and FCS Express will pause according to the conditional option that was selected. This will give the user the opportunity to review data that satisfies the condition set according to the options selected.


When to use Review for batch processing:

If data needs to re-analyzed or was earmarked for review, but the data does not need to re-exported as part of the batch processing export products, or, If Iteration Snapshots were applied and data needs to be reviewed for a condition or if earmarked for review, but does not need to be re-exported as part of the batch processing export products.

Applications Example: In the example below, we will choose the Review mode to review one of the 10 color samples that was flagged in FCS Express for review. The Batch Actions will not be performed but snapshots that were recorded will be applied during the review process. Using Review is an ideal way to come back to a sample that was earmarked for further inquiry, either for a supervisor to review a gating strategy or verify samples that were flagged during a prior batch process.