Full Overview: Batch Processing

Batch Processing

Many experiments involve analyzing hundreds of samples using the exact same analysis protocol. To report the results, the scientist usually increments through the samples, writes down the statistics of interest, enters all these statistics into a spreadsheet, and makes calculations. For a simple figure, it may require hours of copying and pasting plots into another third-party software for further formatting. FCS Express saves you from these tedious workflows with powerful batch processing.

With FCS Express, set up your analysis protocol the way you want. Then, run the batch process for the files you wish to analyze, and FCS Express will iterate through all your files using this analysis protocol. You can save the layout as a template to reused when the experiment is repeated. You can choose whether you want all your results printed, saved as images, exported as a PowerPoint presentation, generate an Excel document, or create an image at any resolution, and much more.

In FCS Express Flow IVD, these reports, added as items to the Batch Actions List, can be set to run automatically based upon user-defined criteria. If a condition is met, the action will be run in the batch processing.

Batch Actions

When setting up the batch process, you set up a series of Actions and Reports, which will be performed every time FCS Express changes the data files. The image below illustrates the actions that are available.

You can see that there are many types of actions that can be performed. You can export results to Excel, create PDF files, print to different printers, Export to Text Files and Export to Word. In addition, you can also save your layout, save to PowerPoint, and save pictures.

Options for Batch Actions

Batch Process Creation

Report Examples

If there are certain statistics you are interested in, you can tell FCS Express to export those statistics though every iteration of the batch process. You can decide if you want those results exported to Excel in a simple table, to Excel in a sophisticated report, to Word in a mail merge process, or to a field in a PDF form. Below is an example of an Excel report with images of plots, metadata, and statistics inserted into specified cells of a spreadsheet.

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

Please expand each section to learn when and how to use each mode.

Run Mode

I am analyzing a data set, and I would like FCS Express to export the results for each sample via batch actions.

In the example below, we have a layout that contains three different 10-color samples 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, enabling us to adjust the gating strategy during the batch process.

Use Run when performing the initial batch processing run for a data set or to overwrite the original Snapshots recorded during the first batch process.

Rerun Mode

I have previously run the batch process on a data set, but I realized that I need to adjust gates, markers, or quads for some samples. I need to go back, make adjustments and export the new and updated results.

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.

Use Rerun if data need to be re-analyzed and results re-exported or Iteration Snapshots were applied and results re-exported as part of the batch process.

Review Mode

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.

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.

Use Review if data need to be re-analyzed without re-exporting results or samples have been earmarked for review.

Batch Processing

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

Please expand each section to learn when and how to use each mode.

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