ndev-workflows

Reproducible processing workflows with napari

A re-implementation of napari-workflows with backwards compatibility.

This [napari] plugin was generated with [copier] using the [napari-plugin-template] (2.0.1).

What is ndev-workflows?

ndev-workflows is the workflow backend for napari image processing pipelines. It's a drop-in replacement for napari-workflows by Robert Haase, with these key improvements:

• Safe YAML loading — Uses yaml.safe_load() (no arbitrary code execution)
• Backwards compatible — Automatically loads and migrates legacy napari-workflows files, and detects missing dependencies
• Same API — Most code works without changes
• Future-ready — Designed for upcoming npe2 workflow contributions (WIP), without relying on npe1, napari-time-slicer, and napari-tools-menu for interactivity

Installation

pip install ndev-workflows

If napari is not already installed, you can install ndev-workflows with napari and Qt via:

pip install "ndev-workflows[all]"

Quick Start

from ndev_workflows import Workflow, save_workflow, load_workflow
from skimage.filters import gaussian

# Create workflow
workflow = Workflow()
workflow.set("blurred", gaussian, "input_image", sigma=2.0)
workflow.set("input_image", my_image)

# Execute
result = workflow.get("blurred")

# Save
save_workflow("pipeline.yaml", workflow, name="My Pipeline")

# Load and reuse
loaded = load_workflow("pipeline.yaml")
loaded.set("input_image", new_image)
result = loaded.get("blurred")

YAML Format

Saved workflows use a safe, human-readable format:

name: Nucleus Segmentation
description: Gaussian blur and thresholding
modified: '2025-12-22'

inputs:
  - raw_image

outputs:
  - labels

tasks:
  blurred:
    function: skimage.filters.gaussian
    params:
      arg0: raw_image
      sigma: 2.0

  labels:
    function: skimage.measure.label
    params:
      arg0: blurred

Key features:

• No !python/object tags (safe to share)
• Functions imported by module path
• Params use arg0, arg1, etc. for positional args and keyword names for kwargs

Legacy format: Old napari-workflows YAML files are automatically detected and migrated when loaded.

Important Notes

Function Dependencies

⚠️ Workflows don't bundle functions — they only store module paths. Recipients need the same packages installed.

If loading fails with WorkflowNotRunnableError, install the missing package:

pip install scikit-image  # for skimage functions
pip install napari-segment-blobs-and-things-with-membranes  # for that plugin

Lazy Loading

Inspect workflows without importing functions:

workflow = load_workflow("untrusted.yaml", lazy=True)
print(workflow.tasks)  # Safe - doesn't execute

Integration

Front-end plugins for interactive workflow building:

• napari-assistant
• napari-workflow-optimizer
• napari-workflow-inspector

Works with processing plugins:

• napari-segment-blobs-and-things-with-membranes
• pyclesperanto
• And more!

Contributing

git clone https://github.com/ndev-kit/ndev-workflows.git
cd ndev-workflows
uv venv
.venv\Scripts\activate
uv pip install -e . --group dev
pytest

License

Distributed under the terms of the [BSD-3] license, "ndev-workflows" is free and open source software Fork of napari-workflows by Robert Haase.

Issues

File an issue with your environment details, YAML file (if applicable), and error messages.