Batch processing¶
PanSeg 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 panseg -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
Input paths¶
The input_path of a workflow accepts four shapes:
input_path |
What runs |
|---|---|
| a file | one job, one image |
| a directory of files | one job per file |
| a directory of subdirectories | one job per subdirectory, each is a time series (alphanumeric filename order) |
| a list of files | one job, the files stacked as one time series |
If files and subdirectories are mixed in the same directory, the files are imported and the subdirectories are ignored.
Widget: Export Batch Workflow¶
- Export directory: Select the directory where the workflow will be exported
- Workflow name: Name of the exported workflow file.