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    73 repositories

    • aicsimageio

      Public archive
      Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python
      pythonxarrayscientific-computing
      pythonxarrayscientific-computingimageiobio-formatsdaskimage-metadatamicroscopyscientific-formats
      Python
      •
      Other
      •51•222•2•0•Updated Dec 1, 2025Dec 1, 2025

    • aics_dask_utils

      Public archive
      Utility functions commonly used by AICS projects for interacting with Dask
      Python
      •
      Other
      •0•1•2•0•Updated Dec 1, 2025Dec 1, 2025

    • cell-tracker-gnn

      Public archive
      [ECCV 2022] Official PyTorch implementation of the paper - Graph Neural Network for Cell Tracking in Microscopy Videos
      Python
      •
      Other
      •12•1•0•0•Updated Dec 1, 2025Dec 1, 2025

    • crossmodal

      Public archive
      Cross modal analysis of RNA seq and images
      Python
      •0•0•4•0•Updated Dec 1, 2025Dec 1, 2025

    • mti_nma

      Public archive
      Normal mode analysis worflow
      Python
      •
      Other
      •0•0•3•1•Updated Nov 17, 2025Nov 17, 2025

    • docker_pytorch_extended

      Public archive
      Uses the pytorch docker image to build an extended image with jupyter notebook, and some other python utils
      Dockerfile
      •6•2•5•0•Updated Nov 17, 2025Nov 17, 2025

    • cookiecutter-pypackage

      Public archive
      A cookiecutter template to generate a new Python package.
      Python
      •
      MIT License
      •7•24•1•0•Updated Nov 17, 2025Nov 17, 2025

    • nvidia-docker-stats

      Public archive
      Monitor nvidia gpu unit load associated with docker spawned processes
      Python
      •
      GNU General Public License v3.0
      •13•29•1•2•Updated Nov 17, 2025Nov 17, 2025

    • quilt3distribute

      Public archive
      People commonly work with tabular datasets, people want to share their data, this makes that easier through Quilt3.
      Python
      •
      Other
      •1•5•6•0•Updated Nov 17, 2025Nov 17, 2025

    • czifile

      Public archive
      czi reader from https://www.lfd.uci.edu/~gohlke/code/czifile.py.html
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •7•15•3•1•Updated Oct 15, 2025Oct 15, 2025

    • pytorch_fnet

      Public archive
      Three dimensional cross-modal image inference
      Python
      •
      Other
      •68•161•34•1•Updated Oct 15, 2025Oct 15, 2025

    • CVAE_testbed

      Public archive
      A research testbed on conditional variational autoencoders using Gaussian distributions as input
      Jupyter Notebook
      •
      Other
      •2•3•0•2•Updated Oct 15, 2025Oct 15, 2025

    • brightfield2fish

      Public archive
      Python
      •
      Other
      •0•2•5•0•Updated Oct 15, 2025Oct 15, 2025

    • DLITE

      Public archive
      Let's infer the forces that cells generate during time series by looking at the angles they make with each other.
      Jupyter Notebook
      •
      Other
      •3•9•1•3•Updated Oct 15, 2025Oct 15, 2025

    • diffusive_distinguishability

      Public archive
      Simulation of homogeneous diffusion, bayesian estimation of underlying diffusion constant, and analysis of distinguishability between diffusivity estimates
      bayesian-inferencetrajectory-analysisdiffusion
      bayesian-inferencetrajectory-analysisdiffusionsingle-particle-motion
      Jupyter Notebook
      •
      Other
      •1•3•0•0•Updated Oct 15, 2025Oct 15, 2025

    • seq2loc

      Public archive
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•3•4•0•Updated Oct 15, 2025Oct 15, 2025

    • fish_morphology_code

      Public archive
      Basic code and automated workflows to produce analysis friendly data from annotated FISH images
      Python
      •
      Other
      •2•4•5•4•Updated Oct 15, 2025Oct 15, 2025

    • QuiltLoader

      Public archive
      Adding custom attributes to quilt nodes
      Python
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Oct 15, 2025Oct 15, 2025

    • napari-annotation-tools

      Public archive
      Python
      •
      Other
      •0•5•3•0•Updated Oct 15, 2025Oct 15, 2025

    • long-term-eng

      Public archive
      Long Term Engineering + Infrastructure Projects
      0•1•4•0•Updated Oct 15, 2025Oct 15, 2025

    • fish_morphology_manuscript_notebooks

      Public archive
      Notebooks for figures in our manuscript
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Oct 15, 2025Oct 15, 2025

    • AllenCellModeling.github.io

      Public archive
      Data stories
      Jupyter Notebook
      •
      MIT License
      •6•10•4•0•Updated Oct 15, 2025Oct 15, 2025

    • datastep

      Public archive
      A base class and utility functions for creating pure functions steps for DAGs.
      Python
      •
      Other
      •0•1•6•0•Updated Oct 15, 2025Oct 15, 2025

    • actk

      Public archive
      Automated Cell Toolkit
      pipelinebiologyimage-processing
      pipelinebiologyimage-processingmicroscopycell-biology
      Python
      •
      Other
      •4•24•3•1•Updated Oct 15, 2025Oct 15, 2025

    • napari-aicsimageio

      Public archive
      Multiple file format reading directly into napari using pure Python
      imageiomicroscopynapari
      imageiomicroscopynapari
      Python
      •
      GNU General Public License v3.0
      •12•38•17•3•Updated Oct 15, 2025Oct 15, 2025

    • cookiecutter-stepworkflow

      Public archive
      AICS Cookiecutter Template for a simple data + code workflow
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 15, 2025Oct 15, 2025

    • pytorch_integrated_cell

      Public archive
      Integrated Cell project implemented in pytorch
      pythonmachine-learningpytorch
      pythonmachine-learningpytorchgenerative-adversarial-networkneural-networksautoencoderscience-researchcell-analysiscell-biology
      Python
      •13•44•27•4•Updated Oct 15, 2025Oct 15, 2025

    • bioloaders

      Public archive
      A repository of dataset objects for common datatypes in bio sciences.
      Python
      •
      Other
      •3•1•0•2•Updated Oct 15, 2025Oct 15, 2025

    • aics-deformation

      Public archive
      Tools to use when working on deformation projects.
      Python
      •
      Other
      •0•1•0•0•Updated Oct 15, 2025Oct 15, 2025

    • torch_integrated_cell

      Public archive
      machine-learningneural-networktorch
      machine-learningneural-networktorchcell-analysisbiolog
      Jupyter Notebook
      •9•46•0•0•Updated Oct 15, 2025Oct 15, 2025
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