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    36 repositories

    • micro_status

      Public
      Checking RSCM imaging and processing status
      Python
      •0•0•0•3•Updated Apr 16, 2026Apr 16, 2026

    • micro_status_flask

      Public
      Dashboard for microscope acquisition monitoring
      Python
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • mesospim_utils

      Public
      Utilities to deal with mesospim data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Apr 13, 2026Apr 13, 2026

    • BrAinPI

      Public
      Development of API for access to BIL datasets
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•5•1•1•Updated Apr 8, 2026Apr 8, 2026

    • zarr_stores

      Public
      A repository for development of custom zarr storage classes
      Python
      •0•4•0•0•Updated Apr 8, 2026Apr 8, 2026

    • omezarr_to_ims

      Public
      A Library for presenting ome-zarr as ims files as a fuse mount
      Python
      •0•0•0•0•Updated Mar 31, 2026Mar 31, 2026

    • ome_zarr_multiscale_writer

      Public
      A OME Zarr writer that builds multiscales on the fly and can be used for microscope data acquisition
      Python
      •0•0•0•0•Updated Mar 27, 2026Mar 27, 2026

    • mesoSPIM-control

      Public
      Image acquisition software for mesoSPIM light-sheet microscopes.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •17•0•0•0•Updated Mar 25, 2026Mar 25, 2026

    • sam_adapter

      Public
      SAM Infrerence API
      Python
      •0•0•0•0•Updated Mar 23, 2026Mar 23, 2026

    • webknossos

      Public
      Visualize, share and annotate your large 3D images online
      TypeScript
      •
      GNU Affero General Public License v3.0
      •34•0•0•0•Updated Mar 23, 2026Mar 23, 2026

    • flask_file_browser

      Public
      file browser for BrAinPI
      CSS
      •1•0•0•0•Updated Jan 29, 2026Jan 29, 2026

    • cfos_morphine_pipeline

      Public
      Workflow for mapping neuronal activation in whole mouse brains
      Jupyter Notebook
      •0•0•0•0•Updated Dec 5, 2025Dec 5, 2025

    • mesospim-plugins

      Public
      A repository for mesospim-plugins
      Python
      •0•1•0•0•Updated Dec 2, 2025Dec 2, 2025

    • test_code_ai

      Public
      test_repo_for_agenic_coding
      0•0•0•0•Updated Nov 30, 2025Nov 30, 2025

    • fli_conversion

      Public
      fli to omehans
      Python
      •0•0•0•0•Updated Nov 26, 2025Nov 26, 2025

    • mesospim_plugin_registry

      Public
      A Public Registry for MesoSPIM Plugins
      Python
      •0•0•0•0•Updated Nov 15, 2025Nov 15, 2025

    • holis_tools

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 1, 2025Oct 1, 2025

    • imaris_ims_file_reader

      Public
      Imaris file format reader
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•15•2•1•Updated Aug 20, 2025Aug 20, 2025

    • urlshortener

      Public
      Python flask-based web tool for shortening urls
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 11, 2025Aug 11, 2025

    • v3d-py-helper

      Public
      Make Vaa3D functions accessible for high-performance python computation.
      Cython
      •
      MIT License
      •1•0•0•0•Updated May 30, 2025May 30, 2025

    • decon_tools

      Public
      A package to do deconvolution accross arbitrarily large datasets
      0•0•0•0•Updated Apr 2, 2025Apr 2, 2025

    • olympus_vs200

      Public
      Python
      •1•0•0•0•Updated Feb 24, 2025Feb 24, 2025

    • virtualhe_rust

      Public
      Virtual H&E image from fluorescent microscopy written in rust
      Rust
      •0•0•0•0•Updated Jan 8, 2025Jan 8, 2025

    • virtualhe_py

      Public
      Virtual H&E image from fluorescent microscopy
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 7, 2025Jan 7, 2025

    • ImarisFileConverter_wine

      Public
      Imaris File Converter for wine on Linux
      1•0•0•0•Updated Dec 4, 2024Dec 4, 2024

    • windows

      Public
      Windows inside a Docker container.
      Shell
      •
      MIT License
      •4.2k•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • holis_mri_images

      Public
      0•0•0•0•Updated Oct 15, 2024Oct 15, 2024

    • PSFmodels

      Public
      Python bindings for scalar and vectorial models of the 3D microscope point spread function.
      C++
      •
      GNU General Public License v3.0
      •11•0•0•0•Updated May 20, 2024May 20, 2024

    • stack_to_multiscale_ngff

      Public
      Convert an image stack to multiscale OME-NGFF Zarr
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•5•1•0•Updated Sep 18, 2023Sep 18, 2023

    • compression_tools

      Public
      Repository for tools to assist in compressing data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Aug 11, 2023Aug 11, 2023
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