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@AllenCell

Allen Institute for Cell Science

Allen Institute Open Source projects for general use.

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  1. aics-ml-segmentation aics-ml-segmentation Public

    Python 32 10

  2. cyto-dl cyto-dl Public

    Python 30 9

  3. aics-segmentation aics-segmentation Public

    Part 1 of Allen Cell and Structure Segmenter: classic image segmentation workflow

    Jupyter Notebook 25 14

  4. cvapipe_analysis cvapipe_analysis Public

    Analysis of data produced by cvapipe for the variance paper

    Jupyter Notebook 24 7

  5. aics-shparam aics-shparam Public

    Python 22 6

  6. napari-allencell-segmenter napari-allencell-segmenter Public

    A plugin that enables image segmentation provided by Allen Institute for Cell Science

    Python 18 6

Repositories

Showing 10 of 37 repositories
  • cellpack-client Public

    Frontend interface for cellPACK

    AllenCell/cellpack-client’s past year of commit activity
    TypeScript 0 0 11 4 Updated Feb 27, 2026
  • ome-zarr-vole-tools Public

    CLI tool to convert microscopy images (TIFF, CZI, ND2, LIF, DV) to OME-Zarr format and generate VolE viewer URLs. Supports batch processing, multi-resolution pyramids, and configurable chunking/compression.

    AllenCell/ome-zarr-vole-tools’s past year of commit activity
    Python 0 0 0 0 Updated Feb 27, 2026
  • idea-board Public
    AllenCell/idea-board’s past year of commit activity
    TypeScript 0 0 16 5 Updated Feb 26, 2026
  • cell-catalog Public

    Cell catalog 2.0

    AllenCell/cell-catalog’s past year of commit activity
    TypeScript 0 MIT 0 13 2 Updated Feb 24, 2026
  • reusable-workflows Public
    AllenCell/reusable-workflows’s past year of commit activity
    0 0 0 0 Updated Feb 20, 2026
  • EMT_data_analysis Public

    This repo contains code for EMT deliverable data analysis and has dependencies associated with output from EMT_image_analysis repo.

    AllenCell/EMT_data_analysis’s past year of commit activity
    Python 1 0 6 2 Updated Feb 18, 2026
  • camera-alignment-core Public

    Core algorithms for alignment of two-camera microscopy imagery

    AllenCell/camera-alignment-core’s past year of commit activity
    Python 0 1 5 0 Updated Jan 27, 2026
  • EMT_image_analysis Public

    Repository for EMT image analysis code

    AllenCell/EMT_image_analysis’s past year of commit activity
    Python 1 2 0 0 Updated Jan 22, 2026
  • nuc-morph-analysis Public
    AllenCell/nuc-morph-analysis’s past year of commit activity
    Python 1 0 1 0 Updated Jan 6, 2026
  • cyto-dl Public
    AllenCell/cyto-dl’s past year of commit activity
    Python 30 9 10 9 Updated Dec 1, 2025
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