Skip to content

@AllenCell Allen Institute for Cell Science

Change the repository type filter

All

    Repositories list

    31 repositories

    • allencell-segmenter-ml

      Public
      Napari plugin for ml segmentation
      Python
      •
      Other
      •1•2•159•1•Updated Feb 17, 2025Feb 17, 2025

    • aics-shparam

      Public
      Python
      •
      Other
      •4•20•0•1•Updated Feb 15, 2025Feb 15, 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•1•0•Updated Feb 12, 2025Feb 12, 2025

    • benchmarking_representations

      Public
      Benchmarking different methods for extracting unsupervised representations from images
      Python
      •
      Other
      •1•2•5•0•Updated Feb 10, 2025Feb 10, 2025

    • nuc-morph-analysis

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • EMT_image_analysis

      Public
      Repository for EMT image analysis code
      Python
      •
      Other
      •0•1•5•2•Updated Jan 23, 2025Jan 23, 2025

    • cvapipe_analysis

      Public
      Analysis of data produced by cvapipe for the variance paper
      Jupyter Notebook
      •
      Other
      •6•22•1•2•Updated Dec 23, 2024Dec 23, 2024

    • i2k_workshop_2024

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

    • camera-alignment-core

      Public
      Core algorithms for alignment of two-camera microscopy imagery
      Python
      •
      Other
      •1•0•5•3•Updated Oct 4, 2024Oct 4, 2024

    • open-data-registry

      Public
      A registry of publicly available datasets on AWS
      Python
      •
      Apache License 2.0
      •952•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•3•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
      •12•28•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

    • aics-cytoparam

      Public
      Python
      •
      Other
      •1•7•2•0•Updated Apr 6, 2024Apr 6, 2024

    • segmenter_model_zoo

      Public
      scripts and API for running Deep Learning models from segmenter
      Jupyter Notebook
      •
      Other
      •1•10•2•2•Updated Dec 6, 2023Dec 6, 2023

    • napari-allencell-segmenter

      Public
      A plugin that enables image segmentation provided by Allen Institute for Cell Science
      napari-pluginnapari-allencell-segmenternapari
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•16•18•1•Updated Nov 28, 2023Nov 28, 2023

    • serotiny

      Public
      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
      Python
      •
      Other
      •1•5•0•0•Updated Dec 7, 2022Dec 7, 2022

    • cytodata-hackathon-base

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

    • cytodata-3d-shape-analysis

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

    • aics-ml-segmentation

      Public
      Python
      •
      Other
      •8•31•7•2•Updated Aug 15, 2022Aug 15, 2022

    • cardio_scrnaseq_paper_code

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

    • image_classifier_3d

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

    • quilt-data-access-tutorials

      Public
      A collection of tutorials for accessing allen cell quilt packages
      Jupyter Notebook
      •2•5•1•0•Updated Apr 9, 2021Apr 9, 2021

    • colony-processing

      Public
      code for 12X colony image processing, dataset creatation and analysis
      Jupyter Notebook
      •0•2•0•0•Updated Feb 15, 2021Feb 15, 2021

    • cvapipe

      Public
      Cell Variance Analysis Pipeline
      Python
      •
      Other
      •0•2•6•0•Updated Dec 7, 2020Dec 7, 2020

    • aicsfeature

      Public
      a central code base for cell feature calculate in different applications
      Python
      •
      Other
      •0•2•0•0•Updated Dec 7, 2020Dec 7, 2020

    • cvapipe_figure_notebooks

      Public
      Notebooks for reproducing figures in the cell variance paper
      Jupyter Notebook
      •0•4•0•0•Updated Dec 6, 2020Dec 6, 2020