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@janelia-cellmap

CellMap Project Team

Using computer vision and machine learning techniques to scalably detect subcellular structures, such as organelles, in datasets generated with next-gen vEM

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  1. dacapo dacapo Public

    A framework for easy application of established machine learning techniques on large, multi-dimensional images.

    Python 60 10

  2. cellmap-models cellmap-models Public

    Repository of model architectures and network weights used for CellMap segmentations.

    Python 13

  3. cellmap-data cellmap-data Public

    Utility for loading CellMap data for machine learning training, utilizing PyTorch, TensorStore, Xarray, and PyDantic.

    Python 7 2

  4. cellmap-segmentation-challenge 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 models, workflows for prediction and post…

    Python 39 16

  5. LeibNetz LeibNetz Public

    A lightweight and modular library for rapidly developing and constructing PyTorch models deep learning.

    Python 2

Repositories

Showing 10 of 72 repositories
  • 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 models, workflows for prediction and post-processing on out-of-memory arrays, and evaluation of results against validation data.

    janelia-cellmap/cellmap-segmentation-challenge’s past year of commit activity
    Python 39 BSD-3-Clause 16 7 4 Updated Dec 22, 2025
  • cellmap-data Public

    Utility for loading CellMap data for machine learning training, utilizing PyTorch, TensorStore, Xarray, and PyDantic.

    janelia-cellmap/cellmap-data’s past year of commit activity
    Python 7 BSD-3-Clause 2 4 (1 issue needs help) 0 Updated Dec 22, 2025
  • frx-challenges Public Forked from 2i2c-org/frx-challenges

    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 science challenges. FRX stands for Frictionless Reproducibility eXchange. Inspired by Donoho, 2023. This project enables communities to host data challenges with live evaluation.

    janelia-cellmap/frx-challenges’s past year of commit activity
    CSS 1 BSD-3-Clause 5 0 0 Updated Dec 19, 2025
  • cellmap-analyze Public
    janelia-cellmap/cellmap-analyze’s past year of commit activity
    Python 3 BSD-3-Clause 0 0 0 Updated Dec 17, 2025
  • cellmap-flow Public

    Utility for visualizing results on the fly in neuroglancer

    janelia-cellmap/cellmap-flow’s past year of commit activity
    Python 7 BSD-3-Clause 1 5 5 Updated Dec 16, 2025
  • zarrify Public

    A simple tool to convert datasets stored in different image formats to zarr array

    janelia-cellmap/zarrify’s past year of commit activity
    Python 2 BSD-3-Clause 1 1 0 Updated Dec 15, 2025
  • openorganelle Public

    A portal for viewing FIB-SEM datasets

    janelia-cellmap/openorganelle’s past year of commit activity
    TypeScript 13 3 26 0 Updated Dec 5, 2025
  • zarr-fractional-rescale Public
    janelia-cellmap/zarr-fractional-rescale’s past year of commit activity
    Python 1 0 0 0 Updated Dec 1, 2025
  • igneous-daskified Public
    janelia-cellmap/igneous-daskified’s past year of commit activity
    Python 3 BSD-3-Clause 0 0 0 Updated Nov 20, 2025
  • LeibNetz Public

    A lightweight and modular library for rapidly developing and constructing PyTorch models deep learning.

    janelia-cellmap/LeibNetz’s past year of commit activity
    Python 2 BSD-3-Clause 0 1 1 Updated Nov 17, 2025
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