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@janelia-cellmap CellMap Project Team

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    80 repositories

    • zarr-fractional-rescale

      Public
      Python
      •0•1•0•0•Updated Apr 24, 2026Apr 24, 2026

    • frx-challenges

      Public
      Welcome to Janelia's fork of the FRX Challenges project! This is an open source repository that provides key software components for running competitive data sc…
      CSS
      •
      BSD 3-Clause "New" or "Revised" License
      •5•1•0•0•Updated Apr 24, 2026Apr 24, 2026

    • cellmap-segmentation-challenge

      Public
      Repository of scripts to facilitate participation in CellMap's segmentation challenge. This includes downloading data, simple setups for training 2D and 3D mode…
      machine-learningbiologyartificial-intelligence
      machine-learningbiologyartificial-intelligencesegmentationzarrome-ngff
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •16•39•5•3•Updated Apr 24, 2026Apr 24, 2026

    • dacapo

      Public
      A framework for easy application of established machine learning techniques on large, multi-dimensional images.
      machine-learningdeep-learningsegmentation
      machine-learningdeep-learningsegmentation
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•60•23•7•Updated Apr 24, 2026Apr 24, 2026

    • cellmap-flow

      Public
      Utility for visualizing results on the fly in neuroglancer
      machine-learningsegmentationneuroglancer
      machine-learningsegmentationneuroglancer
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•8•7•8•Updated Apr 23, 2026Apr 23, 2026

    • zarrify

      Public
      A simple tool to convert datasets stored in different image formats to zarr array
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•1•0•Updated Apr 23, 2026Apr 23, 2026

    • mesh-n-bone

      Public
      Python
      •
      Other
      •2•9•0•0•Updated Apr 17, 2026Apr 17, 2026

    • cellmap-analyze

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•0•0•Updated Apr 17, 2026Apr 17, 2026

    • openorganelle

      Public
      A portal for viewing FIB-SEM datasets
      TypeScript
      •
      Other
      •3•13•26•14•Updated Apr 14, 2026Apr 14, 2026

    • igneous-daskified

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Apr 12, 2026Apr 12, 2026

    • ask-to-mask

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 11, 2026Apr 11, 2026

    • zarr-multiscale

      Public
      Python
      •0•1•0•0•Updated Apr 2, 2026Apr 2, 2026

    • cellmap-challenge-analysis

      Public
      Python
      •0•0•0•0•Updated Mar 24, 2026Mar 24, 2026

    • cellmap-models

      Public
      Repository of model architectures and network weights used for CellMap segmentations.
      machine-learningsegmentation
      machine-learningsegmentation
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•13•1•0•Updated Mar 23, 2026Mar 23, 2026

    • cellmap-data

      Public
      Utility for loading CellMap data for machine learning training, utilizing PyTorch, TensorStore, Xarray, and PyDantic.
      machine-learningndarraydataloader
      machine-learningndarraydataloaderzarr
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•7•3•0•Updated Mar 20, 2026Mar 20, 2026

    • topo

      Public
      Topology-aware diffusion-based flow field generation for 3D instance segmentation
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Mar 17, 2026Mar 17, 2026

    • cellmap-model-kit

      Public
      Export, package, and load PyTorch models for CellMap.
      Python
      •0•0•0•0•Updated Feb 27, 2026Feb 27, 2026

    • exp_mito

      Public
      lsd runs with mito will all crops
      Python
      •0•0•0•0•Updated Feb 18, 2026Feb 18, 2026

    • cellmap-flow-hub

      Public
      Python
      •0•0•0•0•Updated Feb 5, 2026Feb 5, 2026

    • cellmap-n5-to-zarr

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jan 28, 2026Jan 28, 2026

    • exp_salivary

      Public
      Python
      •0•0•0•0•Updated Dec 15, 2025Dec 15, 2025

    • mito_proofread

      Public
      A web-based tool for proofreading mitochondria segmentation skeletons with interactive 3D visualization and Neuroglancer integration.
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 26, 2025Nov 26, 2025

    • LeibNetz

      Public
      A lightweight and modular library for rapidly developing and constructing PyTorch models deep learning.
      machine-learningcnnpytorch
      machine-learningcnnpytorch
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•1•1•Updated Nov 17, 2025Nov 17, 2025

    • exp-overview

      Public
      an overview and reference for the experimental projects
      HTML
      •0•1•0•0•Updated Nov 12, 2025Nov 12, 2025

    • metabolic-liver-zonation

      Public
      Analysis code and workflows for mapping organelle architecture across liver zonation using FIB-SEM. Includes tools for ER–mitochondria contact quantification, m…
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 14, 2025Oct 14, 2025

    • segmentation-challenge-meshes

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated May 23, 2025May 23, 2025

    • openorganelle-blog

      Public
      Periodic content for openorganelle
      BSD 3-Clause "New" or "Revised" License
      •2•0•5•0•Updated Apr 11, 2025Apr 11, 2025

    • fibsem-tools

      Public
      Tools for handling FIB-SEM data and annotations
      Python
      •
      MIT License
      •8•21•9•3•Updated Apr 4, 2025Apr 4, 2025

    • amira_python_extensions

      Public
      Extensions to Amira for reading and writing common array container formats (HDF5, N5)
      Batchfile
      •2•1•0•0•Updated Mar 26, 2025Mar 26, 2025

    • process-blockwise

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•1•0•Updated Jan 10, 2025Jan 10, 2025
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