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    76 repositories

    • cyto-dl

      Public
      Python
      •8•26•10•5•Updated Jul 18, 2025Jul 18, 2025

    • aicspylibczi

      Public
      Python module utilizing libCZI for reading Zeiss CZI files.
      C++
      •
      GNU General Public License v3.0
      •9•39•14•0•Updated Apr 14, 2025Apr 14, 2025

    • fov_processing_pipeline

      Public
      Python
      •
      Other
      •0•0•8•1•Updated Mar 26, 2025Mar 26, 2025

    • aicsimageio

      Public
      Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python
      xarrayscientific-computingimageiobio-formatsdaskimage-metadatamicroscopyscientific-formatspython
      Python
      •
      Other
      •50•215•2•0•Updated Jan 15, 2025Jan 15, 2025

    • czi-to-ome-xslt

      Public
      A repository of XSL transform sheets to map CZI metadata to OME.
      XSLT
      •
      Other
      •0•2•6•0•Updated Dec 13, 2024Dec 13, 2024

    • fish_morphology_code

      Public
      Basic code and automated workflows to produce analysis friendly data from annotated FISH images
      Python
      •
      Other
      •2•4•5•4•Updated Nov 4, 2024Nov 4, 2024

    • napari-aicsimageio

      Public
      Multiple file format reading directly into napari using pure Python
      imageiomicroscopynapari
      Python
      •
      GNU General Public License v3.0
      •12•37•16•3•Updated Jul 21, 2024Jul 21, 2024

    • pointcloudutils

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Apr 17, 2024Apr 17, 2024

    • nvidia-docker-stats

      Public
      Monitor nvidia gpu unit load associated with docker spawned processes
      Python
      •
      GNU General Public License v3.0
      •12•29•1•2•Updated Oct 1, 2023Oct 1, 2023

    • aics_dask_utils

      Public
      Utility functions commonly used by AICS projects for interacting with Dask
      Python
      •
      Other
      •0•1•2•0•Updated Aug 10, 2023Aug 10, 2023

    • aicsimageprocessing

      Public archive
      A generalized scientific image processing module from the Allen Institute for Cell Science.
      Python
      •
      Other
      •1•2•1•1•Updated Aug 2, 2023Aug 2, 2023

    • CVAE_testbed

      Public
      A research testbed on conditional variational autoencoders using Gaussian distributions as input
      Jupyter Notebook
      •
      Other
      •2•3•0•2•Updated Jul 6, 2023Jul 6, 2023

    • DLITE

      Public
      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 Jul 6, 2023Jul 6, 2023

    • pytorch_integrated_cell

      Public
      Integrated Cell project implemented in pytorch
      pythonmachine-learningpytorchgenerative-adversarial-networkneural-networksautoencoderscience-researchcell-analysiscell-biology
      Python
      •13•44•27•4•Updated Jul 6, 2023Jul 6, 2023

    • cell-tracker-gnn

      Public
      [ECCV 2022] Official PyTorch implementation of the paper - Graph Neural Network for Cell Tracking in Microscopy Videos
      Python
      •
      Other
      •12•1•0•0•Updated Jan 30, 2023Jan 30, 2023

    • bioloaders

      Public
      A repository of dataset objects for common datatypes in bio sciences.
      Python
      •
      Other
      •3•1•0•2•Updated Oct 27, 2022Oct 27, 2022

    • serotiny-tests

      Public archive
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 25, 2022Oct 25, 2022

    • serotiny-project-cookiecutter

      Public archive
      a cookiecutter to set up serotiny templates
      1•0•0•0•Updated Oct 24, 2022Oct 24, 2022

    • crossmodal

      Public
      Cross modal analysis of RNA seq and images
      Python
      •0•0•4•0•Updated Oct 11, 2022Oct 11, 2022

    • quilt3distribute

      Public
      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 Jul 22, 2022Jul 22, 2022

    • aicsimageio-ometiffreader

      Public
      ome tiff reader for aicsimageio
      Python
      •
      Other
      •0•0•0•0•Updated Jul 18, 2022Jul 18, 2022

    • libCZI

      Public
      Open Source Cross-Platform C++ library to read CZI image files
      C++
      •
      GNU General Public License v3.0
      •19•0•0•0•Updated Dec 15, 2021Dec 15, 2021

    • timelapse_tools

      Public
      Load and convert 🎥
      Python
      •
      Other
      •0•0•0•1•Updated Oct 27, 2021Oct 27, 2021

    • mti_nma

      Public
      Normal mode analysis worflow
      Python
      •
      Other
      •0•0•3•1•Updated Aug 16, 2021Aug 16, 2021

    • ColabNotebookExamples

      Public
      Colab Notebooks with example deep learning experiments using AICS data
      Jupyter Notebook
      •0•0•0•0•Updated Mar 2, 2021Mar 2, 2021

    • fish_morphology_manuscript_notebooks

      Public
      Notebooks for figures in our manuscript
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Feb 11, 2021Feb 11, 2021

    • napari-annotation-tools

      Public
      Python
      •
      Other
      •0•5•3•0•Updated Feb 10, 2021Feb 10, 2021

    • cookiecutter-pypackage

      Public
      A cookiecutter template to generate a new Python package.
      Python
      •
      MIT License
      •7•23•1•0•Updated Jan 24, 2021Jan 24, 2021

    • cookiecutter-stepworkflow

      Public
      AICS Cookiecutter Template for a simple data + code workflow
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 4, 2021Jan 4, 2021

    • actk

      Public
      Automated Cell Toolkit
      biologyimage-processingmicroscopycell-biologypipeline
      Python
      •
      Other
      •4•24•3•1•Updated Dec 15, 2020Dec 15, 2020