pisco-segmenter-py 0.1.0

PISCO image segmentation pipeline

pisco_segmenter_py

Standalone, pip-installable segmentation package used by process_pisco_profiles.

Install

# after publishing on PyPI
pip install pisco_segmenter_py

# local development install
pip install -e .

Usage

from pisco_segmenter import run_segmenter

run_segmenter("/path/to/images", "/path/to/output", deconvolution=True)

Deconvolution model path

By default, deconvolution expects a model under:

pisco_segmenter/models/lucyd-edof-plankton_231204.pth

You can override this with:

PISCO_SEGMENTER_MODEL_PATH=/abs/path/to/model.pth