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    76 repositories

    • camacq-plugins

      Public
      Plugins for camacq
      Python
      •
      Apache License 2.0
      •0•0•0•21•Updated Aug 4, 2026Aug 4, 2026

    • cam_acq

      Public
      Python project to control microscope through client-server program.
      Python
      •
      Apache License 2.0
      •0•5•1•22•Updated Aug 4, 2026Aug 4, 2026

    • subcell-embed

      Public
      Codebase for training the SubCell models
      Python
      •
      MIT License
      •3•24•0•0•Updated Aug 3, 2026Aug 3, 2026

    • seq2loc_benchmark

      Public
      Code for "A comprehensive benchmark of sequence-based subcellular localization predictors for human proteins"
      Jupyter Notebook
      •
      MIT License
      •0•5•1•0•Updated Jul 30, 2026Jul 30, 2026

    • subcell-analysis

      Public
      Jupyter Notebook
      •
      MIT License
      •1•17•0•0•Updated Jul 29, 2026Jul 29, 2026

    • CellposeSegmentatorPortable

      Public
      Simple wrapper that runs Cellpose segmentation model in a convenient way. It can run nuclei, nuclei + cytoplasm or nuclei + 2 x cytoplasm [combined] segmentatio…
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 20, 2026Jul 20, 2026

    • pipex

      Public
      A pipeline to transform images into valuable analysis items
      Python
      •
      MIT License
      •2•19•0•0•Updated Jul 17, 2026Jul 17, 2026

    • ell_code_template

      Public
      Python
      •
      MIT License
      •1•0•0•0•Updated Jul 17, 2026Jul 17, 2026

    • HPACellSegmentatorPortable

      Public
      Just a rework of the HPA Cell Segmentator repository that works with modern and simple python libraries
      Python
      •0•0•0•1•Updated Jul 17, 2026Jul 17, 2026

    • SubCellPortable

      Public
      This is a convenient code wrapper to run Lundberg lab SubCell model in inference with your own images
      Python
      •
      MIT License
      •6•9•0•0•Updated Jul 16, 2026Jul 16, 2026

    • HPA_BleedThrough_Exploration

      Public
      Code for exploring whether bleed through exists in HPA data
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 9, 2026Jul 9, 2026

    • hpaseg

      Public
      HPAseg is a batch segmentation and single-cell quantification tool for HPA-style brightfield IHC images (RGB images stained with hematoxylin for nuclei and DAB …
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 1, 2026Jul 1, 2026

    • pyshowwwcase

      Public
      PyShowwwcase is a reusable Django front-end for batch processing pipelines
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jul 1, 2026Jul 1, 2026

    • ellviewer

      Public
      Simple and configurable layered viewer, serverless and zero-code configurable
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jul 1, 2026Jul 1, 2026

    • ell_espace

      Public
      Collection of scripts used to annotate and analyze spatial proteomics data for the ESPACE project (non-diseased pancreatic tissue)
      Python
      •0•0•0•0•Updated Jun 27, 2026Jun 27, 2026

    • HPA_Convert_Sp8_To_OMETIF

      Public
      FIJI plugin that allows to convert the ome.tif files exported from the 3D viewer in Leica's LASX (Confocal Microscope DMi8-Sp8 or Stellaris 8) to metadata-rich …
      Java
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jun 23, 2026Jun 23, 2026

    • ProtiCelli

      Public
      Group-wise release of ProtiCelli, including core code deveplopment.
      Python
      •6•24•0•0•Updated Jun 12, 2026Jun 12, 2026

    • memento

      Public
      A simple tool for sharing and annotate images
      Python
      •
      MIT License
      •0•1•0•0•Updated May 18, 2026May 18, 2026

    • 2dShapeSpacePortable

      Public
      2dShapeSpacePortable is a pipeline for quantifying the shape of cells and nuclei from 2D fluorescence microscopy images and mapping how proteins distribute with…
      Python
      •
      MIT License
      •1•1•0•0•Updated Apr 29, 2026Apr 29, 2026

    • gui_for_wet_lab

      Public
      Simple GUI tools to for wet-lab experiment and sample preparation
      HTML
      •
      MIT License
      •0•1•0•0•Updated Apr 3, 2026Apr 3, 2026

    • HPA_Convert_OPERA_To_LIMS-OMETIF

      Public
      An ImageJ plugin to convert Opera Phenix image output folders to OME Tif format suitable for the HPA LIMS system or for Memento.
      Java
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Mar 6, 2026Mar 6, 2026

    • HPA_SingleCellClassification_Analysis

      Public
      Analysis for Kaggle Human Protein Atlas Single Cell Classification challenge and 1st place solution
      Python
      •1•1•0•0•Updated Feb 10, 2026Feb 10, 2026

    • 2D_shapespace

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Feb 10, 2026Feb 10, 2026

    • CAR-TCell-MPX-Analysis

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Jan 23, 2026Jan 23, 2026

    • TifCs_To_HPA-PNG-JPEG

      Public
      FIJI plugin that reads folders with single-channel tif files and outputs an identical file system with PNGs and JPEGs in HPA-Style.
      Java
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 3, 2025Dec 3, 2025

    • Biomni_MCP

      Public
      Python
      •0•0•0•0•Updated Sep 23, 2025Sep 23, 2025

    • Sp8-Lif_To_Memento

      Public
      FIJI plugin that allows to read .lif files from Leica microscopes and outputs a file system with JPG files, PNGs, TIFs, or Multi-plane TIF stacks (for use in Me…
      Java
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Sep 23, 2025Sep 23, 2025

    • HPA_Cilia_Study_Code

      Public
      Code underpinning data processing and analysis in the preprint https://www.biorxiv.org/content/10.1101/2024.10.20.619273.
      primary-ciliahuman-protein-atlas
      primary-ciliahuman-protein-atlas
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Sep 23, 2025Sep 23, 2025

    • Squid

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •56•0•0•0•Updated Sep 10, 2025Sep 10, 2025

    • image-stitcher

      Public
      stitching together 5D OME-zarr from an input folder of microscope acquisition images
      Python
      •6•0•0•0•Updated Sep 8, 2025Sep 8, 2025
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