Working with workflows

PanSeg can create and execute workflows for batch processing. A new workflow can be created in the napari gui, and it can be executed using the commandline interface.

Creating a workflow

To create a new workflow, one must process an example image through the napari GUI. Once the result has been exported, a button to Export Workflow will appear in the input/output tab in napari. PanSeg then creates a yaml file to repeat the workflow for any number of files.

The workflow includes input/output paths and naming schemes, so before the new workflow is useable, those need to be adjusted using the editor:

Editing a workflow

PanSeg comes with an editor for the workflow yaml files. It can be opened through the napari gui (Edit Workflow), or from the cli:

panseg --editor [workflow.yaml]

Input/Output

On the left, the input/output section is shown. The input_path field accepts the same shapes as the batch processing runner: a single file, a directory of files (one job per file), a directory of subdirectories (one job per subdirectory), or a list of files (stacked as one time series). Pick several files at once in the Select files dialog, or type a directory path into the field.

A workflow file whose inputs section holds a list of several input sets is a headless batch configuration. The editor does not open those; run them with panseg --config.

The name_pattern defines how the exported images are named. You can use the placeholders {file_name} to reference the input file's name, or {image_name} to reference the layer name napari would have given the image.

Tasks

The right side displays all tasks the workflow contains. Most of them expose some modifiable values.

If you need to modify something else, the editor should show you the proper name of the field, so you can edit the file in your favorite text editor.

Running a workflow

To finally run a workflow after you have modified the paths to your liking, please use the cli:

panseg --config your_workflow_file.yaml