janelia-cellmap/cellmap-segmentation-challenge
Repository of scripts to facilitate participation in CellMap's segmentation challenge. This includes downloading data, simple setups for training 2D and 3D models, workflows for prediction and post-processing on out-of-memory arrays, and evaluation of results against validation data.
This toolbox helps biologists and researchers participating in the CellMap Segmentation Challenge. It simplifies the entire workflow, from downloading large microscopy image datasets of cells to training and evaluating custom cell segmentation models. You input raw imaging data and your model choices, and it outputs segmented cell structures and performance metrics.
Use this if you are a researcher or scientist involved in cell imaging and need to develop, train, and evaluate machine learning models for segmenting cellular structures from electron microscopy data for the CellMap Challenge.
Not ideal if you are looking for a pre-trained, ready-to-use cell segmentation application without needing to train custom models or if you are not working with CellMap Challenge data.
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40
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16
Language
Python
License
BSD-3-Clause
Category
Last pushed
Mar 06, 2026
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