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How-to Guides

This section is dedicated to experienced users. If you are new to this project, please take a look at the tutorial section first.

Important

All commands are run from within the project root directory.

Documentation

Build Documentation

An offline version of the documentation can be built with the following command: 

pixi run build_docs

Serve Documentation

A mkdocs server can be started to serve the documentation website. This is useful if you are actively working on the documentation and want to see live changes. Use the following command: 

pixi run show_docs

Data Processing

Build Config

Build the acquisition_config.yaml file and store it in the working directory WD:

WD=runs/dataset-name pixi run build_config

$env:WD='runs/dataset-name'; pixi run build_config

set WD=runs/dataset-name
pixi run build_config

Replace dataset-name with the name of the dataset you would like to process.

Run Segment

Run the segmentation step, with the acquisition_config.yaml stored in WD, manually:

WD=runs/dataset-name pixi run segment

$env:WD='runs/dataset-name'; pixi run segment

set WD=runs/dataset-name
pixi run segment

Run Measure

Run the measure step, with the measure_config.yaml stored in WD, manually:

WD=runs/dataset-name pixi run measure

$env:WD='runs/dataset-name'; pixi run measure

set WD=runs/dataset-name
pixi run measure

Visualize Results

Run jupyter lab with the visualization jupyter notebook inside WD:

WD=runs/dataset-name pixi run visualize

$env:WD='runs/dataset-name'; pixi run visualize

set WD=runs/dataset-name
pixi run visualize

Run Workflow

Instead of calling the processing steps manually, you can call the nextflow workflow with:

WD=runs/dataset-name pixi run nextflow

Nextflow is not available on Windows.

Nextflow is not available on Windows.

Development

Jupyter Lab

Run jupyter lab to develop new notebooks: 

pixi run jupyter

Napari

Run napari to visualize data: 

pixi run napari

Lint

Clean up code formatting: 

pixi run lint