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    38 repositories

    • idea-board

      Public
      TypeScript
      •
      Other
      •0•0•13•4•Updated Apr 30, 2026Apr 30, 2026

    • cellpack-client

      Public
      Frontend interface for cellPACK
      TypeScript
      •
      Other
      •0•0•8•2•Updated Apr 29, 2026Apr 29, 2026

    • slurm-monitor

      Public
      Lightweight SLURM resource usage monitoring for aics and aics_gpu partitions
      Python
      •0•0•0•0•Updated Apr 29, 2026Apr 29, 2026

    • cell-catalog

      Public
      Cell catalog 2.0
      TypeScript
      •
      MIT License
      •0•0•11•2•Updated Apr 28, 2026Apr 28, 2026

    • cyto-dl

      Public
      Python
      •9•30•10•9•Updated Mar 23, 2026Mar 23, 2026

    • reusable-workflows

      Public
      0•0•0•0•Updated Feb 20, 2026Feb 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.
      Python
      •
      Other
      •0•1•6•0•Updated Feb 18, 2026Feb 18, 2026

    • camera-alignment-core

      Public
      Core algorithms for alignment of two-camera microscopy imagery
      Python
      •
      Other
      •1•0•5•0•Updated Jan 27, 2026Jan 27, 2026

    • EMT_image_analysis

      Public
      Repository for EMT image analysis code
      Python
      •
      Other
      •2•1•0•0•Updated Jan 22, 2026Jan 22, 2026

    • nuc-morph-analysis

      Public
      Python
      •
      Other
      •0•1•1•0•Updated Jan 6, 2026Jan 6, 2026

    • napari-allencell-segmenter

      Public
      A plugin that enables image segmentation provided by Allen Institute for Cell Science
      napari-pluginnaparinapari-allencell-segmenter
      napari-pluginnaparinapari-allencell-segmenter
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•20•18•0•Updated Nov 18, 2025Nov 18, 2025

    • allencell-segmenter-ml

      Public
      Napari plugin for ml segmentation
      Python
      •
      Other
      •2•5•171•1•Updated Nov 7, 2025Nov 7, 2025

    • aics-ml-segmentation

      Public
      Python
      •
      Other
      •11•33•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
      •3•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•4•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
      •6•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
      •16•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

    • 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

    • action-electron-builder

      Public
      :electron: GitHub Action for building and releasing Electron apps
      JavaScript
      •
      MIT License
      •229•0•0•0•Updated Dec 20, 2021Dec 20, 2021
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