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 .

Read more about batch workflows in this chapter.

You find the batch processing section in the output tab in napari!

Warning

Some interactive steps can't be recorded into workflows, especially cropping and proofreading

Widget: Export Batch Workflow

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.