After you have tested and tuned the pipeline on single fields, use the multi‑run functionality to apply it to multiple wells and fields of your well plate dataset. Please note that multi-run execution is only available when the Batch module is available.

Executing on multiple wells

  1. You have configured the pipeline parameters.
  1. Click Multi-run icon in the Pipeline toolbar.
  2. The Run Pipeline on Multiple Wells dialog is displayed.
  3. To select the wells and fields on which the pipeline should be executed, click while pressing SHIFT or CTRL.
  4. Use the Field of all wells function to select the fields on which the analysis pipeline should run.
    Note: It is not possible to choose different fields for different wells, for example field 1 for well A1 and field 3 for well A2. All selected fields must use the same well selection.
  5. To start the multi-run, click Start (n) pipeline runs.

Multi-run status

After starting the multi-run, the Analysis panel is displayed, showing all selected elements (wells and fields).

Progress is shown at different levels with information about waiting and running runs.

The Data Aggregation dialog (see Viewing the results) opens automatically as soon as the first well has finished processing. The finished state of fields is preserved even after closing and reopening the Multi‑run panel. Fields that already contain aggregated data for the current pipeline are treated as "already run" and are not processed again.

In case of success, the icon is shown.

In case of success with errors or warnings, the icon is shown.

In case of failure, the icon is shown.

For more information about the error, hover the mouse over the circle at the top of the panel for a few seconds. A new panel is displayed with additional information. At the top level, errors are grouped at the well level if the same error occurred in multiple fields.