-
Notifications
You must be signed in to change notification settings - Fork 0
Home
Welcome to the PARSEG wiki!
PARSEG (PArallelised Refinement of SEGmentations) is a workflow for the combining of segmentation maps and subsequent removal of overlapping objects. It can be utilised as either a napari plugin for graphical user interaction or as a Python API to be included in custom workflows. This document will describe both implementations.
To use these scripts you need to install napari-segmentation-overlap-filter in a conda environment. For GUI usage, install the plugin in an environment which contains Napari.
Activate the your Napari environment and pip install the plugin
$ conda activate napari-env
$ pip install napari-segmentation-overlap-filter
Download the code into a folder where you want to run it from. All python scripts and jupyter notebooks take path to root directory containing data.
napari-segmentation-overlap-filter combines existing segmentation masks and is agnostic to how these segmentations are created as long as they are labelled images with background pixels assigned as 0. For generating labels with FIJI's Trackmate-Cellpose and using Trackmate_Cellpose_GUI.py see this page.