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    36 repositories

    • cell-catalog

      Public
      Cell catalog 2.0
      TypeScript
      •
      MIT License
      •0•0•23•2•Updated Dec 18, 2025Dec 18, 2025

    • EMT_image_analysis

      Public
      Repository for EMT image analysis code
      Python
      •
      Other
      •2•1•0•0•Updated Dec 18, 2025Dec 18, 2025

    • nuc-morph-analysis

      Public
      Python
      •
      Other
      •0•0•1•1•Updated Dec 17, 2025Dec 17, 2025

    • cellpack-client

      Public
      Frontend interface for cellPACK
      TypeScript
      •
      Other
      •0•0•11•3•Updated Dec 16, 2025Dec 16, 2025

    • EMT_data_analysis

      Public
      This repo contains code for EMT deliverable data analysis and has dependencies associated with output from EMT_image_analysis repo.
      Python
      •
      Other
      •0•1•6•1•Updated Dec 10, 2025Dec 10, 2025

    • idea-board

      Public
      TypeScript
      •
      Other
      •0•0•11•2•Updated Dec 10, 2025Dec 10, 2025

    • cyto-dl

      Public
      Python
      •9•29•10•9•Updated Dec 1, 2025Dec 1, 2025

    • napari-allencell-segmenter

      Public
      A plugin that enables image segmentation provided by Allen Institute for Cell Science
      napari-pluginnaparinapari-allencell-segmenter
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•17•18•0•Updated Nov 18, 2025Nov 18, 2025

    • allencell-segmenter-ml

      Public
      Napari plugin for ml segmentation
      Python
      •
      Other
      •1•3•171•1•Updated Nov 7, 2025Nov 7, 2025

    • camera-alignment-core

      Public
      Core algorithms for alignment of two-camera microscopy imagery
      Python
      •
      Other
      •1•0•5•0•Updated Sep 9, 2025Sep 9, 2025

    • aics-ml-segmentation

      Public
      Python
      •
      Other
      •10•32•7•2•Updated Jul 31, 2025Jul 31, 2025

    • segmenter_model_zoo

      Public
      scripts and API for running Deep Learning models from segmenter
      Jupyter Notebook
      •
      Other
      •2•10•2•2•Updated Jul 30, 2025Jul 30, 2025

    • benchmarking_representations

      Public
      Benchmarking different methods for extracting unsupervised representations from images
      Python
      •
      Other
      •3•6•3•1•Updated Jul 14, 2025Jul 14, 2025

    • aics-cytoparam

      Public
      Python
      •
      Other
      •1•7•2•0•Updated May 1, 2025May 1, 2025

    • aics-shparam

      Public
      Python
      •
      Other
      •5•22•1•0•Updated May 1, 2025May 1, 2025

    • cvapipe_analysis

      Public
      Analysis of data produced by cvapipe for the variance paper
      Jupyter Notebook
      •
      Other
      •7•24•2•2•Updated Dec 23, 2024Dec 23, 2024

    • i2k_workshop_2024

      Public archive
      CytoDL demo for I2K 2024
      Jupyter Notebook
      •0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

    • open-data-registry

      Public
      A registry of publicly available datasets on AWS
      Python
      •
      Apache License 2.0
      •1.1k•0•0•0•Updated Aug 30, 2024Aug 30, 2024

    • PairUPWorkshop

      Public
      Codebase for the PairUP Workshop held at Allen Institute for Cell Science
      Jupyter Notebook
      •
      Other
      •3•4•0•0•Updated Aug 2, 2024Aug 2, 2024

    • aics-segmentation

      Public
      Part 1 of Allen Cell and Structure Segmenter: classic image segmentation workflow
      Jupyter Notebook
      •
      Other
      •14•26•9•0•Updated Jul 22, 2024Jul 22, 2024

    • aics-timelapse-tracking

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jul 16, 2024Jul 16, 2024

    • aics-track-curator

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jul 1, 2024Jul 1, 2024

    • morflowgenesis

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jun 7, 2024Jun 7, 2024

    • on-boarding

      Public
      Python
      •1•0•0•0•Updated Mar 21, 2023Mar 21, 2023

    • serotiny

      Public archive
      Tools for pytorch machine learning pipelines
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•8•1•1•Updated Feb 9, 2023Feb 9, 2023

    • stemcellorganellesizescaling

      Public archive
      Python
      •
      Other
      •2•5•0•0•Updated Dec 7, 2022Dec 7, 2022

    • cytodata-hackathon-base

      Public archive
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •7•1•0•1•Updated Nov 1, 2022Nov 1, 2022

    • cytodata-3d-shape-analysis

      Public archive
      Jupyter Notebook
      •1•4•0•0•Updated Oct 17, 2022Oct 17, 2022

    • cardio_scrnaseq_paper_code

      Public archive
      Jupyter Notebook
      •
      Other
      •0•1•1•0•Updated Aug 6, 2021Aug 6, 2021

    • image_classifier_3d

      Public archive
      Python package for 3D image classification using deep neural network
      Python
      •
      Other
      •1•2•0•0•Updated Jul 31, 2021Jul 31, 2021