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Batch processing

Plantseg supports processing a whole stack of images at once through the use of batch scripts.

To generate such a workflow script, first process one image in the intended way, and export the result. Then, go to the Batch tab in Napari and save the workflow script to a yaml file.

You can review and edit workflow scripts using the build-in workflow editor; open it either directly from the napari Batch tab, or from the command line using plantseg -e .

Widget: Export Batch Workflow

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Save the workflow as a yaml file
  • Export directory: Select the directory where the workflow will be exported
  • Workflow name: Name of the exported workflow file.