Repositories list

• cam_acq

  Public
  Python project to control microscope through client-server program.

  Python

  •

  Apache License 2.0

  •00 forks in CellProfiling/cam_acq•66 stars in CellProfiling/cam_acq•11 issue in CellProfiling/cam_acq•1717 pull requests in CellProfiling/cam_acq•Updated Oct 25, 2026Oct 25, 2026

• camacq-plugins

  Public
  Plugins for camacq

  Python

  •

  Apache License 2.0

  •00 forks in CellProfiling/camacq-plugins•00 stars in CellProfiling/camacq-plugins•00 issues in CellProfiling/camacq-plugins•1919 pull requests in CellProfiling/camacq-plugins•Updated Oct 23, 2026Oct 23, 2026

• subcell-embed

  Public
  Codebase for training the SubCell models

  Python

  •

  MIT License

  •33 forks in CellProfiling/subcell-embed•2525 stars in CellProfiling/subcell-embed•00 issues in CellProfiling/subcell-embed•00 pull requests in CellProfiling/subcell-embed•Updated Oct 19, 2026Oct 19, 2026

• subcell-analysis

  Public
  Jupyter Notebook

  •

  MIT License

  •11 fork in CellProfiling/subcell-analysis•1818 stars in CellProfiling/subcell-analysis•00 issues in CellProfiling/subcell-analysis•00 pull requests in CellProfiling/subcell-analysis•Updated Oct 14, 2026Oct 14, 2026

• pipex

  Public
  A pipeline to transform images into valuable analysis items

  Python

  •

  MIT License

  •22 forks in CellProfiling/pipex•1919 stars in CellProfiling/pipex•00 issues in CellProfiling/pipex•00 pull requests in CellProfiling/pipex•Updated Sep 21, 2026Sep 21, 2026

• ProtiCelli

  Public
  Group-wise release of ProtiCelli, including core code deveplopment.

  Python

  •

  GNU General Public License v3.0

  •66 forks in CellProfiling/ProtiCelli•2929 stars in CellProfiling/ProtiCelli•00 issues in CellProfiling/ProtiCelli•00 pull requests in CellProfiling/ProtiCelli•Updated Sep 15, 2026Sep 15, 2026

• hpa-tissue-ihc-dataset

  Public
  Python

  •

  MIT License

  •00 forks in CellProfiling/hpa-tissue-ihc-dataset•11 star in CellProfiling/hpa-tissue-ihc-dataset•00 issues in CellProfiling/hpa-tissue-ihc-dataset•00 pull requests in CellProfiling/hpa-tissue-ihc-dataset•Updated Sep 7, 2026Sep 7, 2026

• HPACellSegmentatorPortable

  Public
  Just a rework of the HPA Cell Segmentator repository that works with modern and simple python libraries

  Python

  •11 fork in CellProfiling/HPACellSegmentatorPortable•00 stars in CellProfiling/HPACellSegmentatorPortable•00 issues in CellProfiling/HPACellSegmentatorPortable•11 pull request in CellProfiling/HPACellSegmentatorPortable•Updated Aug 14, 2026Aug 14, 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

  •00 forks in CellProfiling/CellposeSegmentatorPortable•00 stars in CellProfiling/CellposeSegmentatorPortable•00 issues in CellProfiling/CellposeSegmentatorPortable•00 pull requests in CellProfiling/CellposeSegmentatorPortable•Updated Aug 14, 2026Aug 14, 2026

• seq2loc_benchmark

  Public
  Code for "A comprehensive benchmark of sequence-based subcellular localization predictors for human proteins"

  Jupyter Notebook

  •

  MIT License

  •00 forks in CellProfiling/seq2loc_benchmark•55 stars in CellProfiling/seq2loc_benchmark•11 issue in CellProfiling/seq2loc_benchmark•00 pull requests in CellProfiling/seq2loc_benchmark•Updated Jul 30, 2026Jul 30, 2026

• ell_code_template

  Public
  Python

  •

  MIT License

  •11 fork in CellProfiling/ell_code_template•00 stars in CellProfiling/ell_code_template•00 issues in CellProfiling/ell_code_template•00 pull requests in CellProfiling/ell_code_template•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

  •66 forks in CellProfiling/SubCellPortable•99 stars in CellProfiling/SubCellPortable•00 issues in CellProfiling/SubCellPortable•00 pull requests in CellProfiling/SubCellPortable•Updated Jul 16, 2026Jul 16, 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

  •00 forks in CellProfiling/hpaseg•00 stars in CellProfiling/hpaseg•00 issues in CellProfiling/hpaseg•00 pull requests in CellProfiling/hpaseg•Updated Jul 1, 2026Jul 1, 2026

• pyshowwwcase

  Public
  PyShowwwcase is a reusable Django front-end for batch processing pipelines

  HTML

  •

  MIT License

  •00 forks in CellProfiling/pyshowwwcase•00 stars in CellProfiling/pyshowwwcase•00 issues in CellProfiling/pyshowwwcase•00 pull requests in CellProfiling/pyshowwwcase•Updated Jul 1, 2026Jul 1, 2026

• ellviewer

  Public
  Simple and configurable layered viewer, serverless and zero-code configurable

  HTML

  •

  MIT License

  •00 forks in CellProfiling/ellviewer•00 stars in CellProfiling/ellviewer•00 issues in CellProfiling/ellviewer•00 pull requests in CellProfiling/ellviewer•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

  •00 forks in CellProfiling/ell_espace•00 stars in CellProfiling/ell_espace•00 issues in CellProfiling/ell_espace•00 pull requests in CellProfiling/ell_espace•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

  •00 forks in CellProfiling/HPA_Convert_Sp8_To_OMETIF•11 star in CellProfiling/HPA_Convert_Sp8_To_OMETIF•00 issues in CellProfiling/HPA_Convert_Sp8_To_OMETIF•00 pull requests in CellProfiling/HPA_Convert_Sp8_To_OMETIF•Updated Jun 23, 2026Jun 23, 2026

• memento

  Public
  A simple tool for sharing and annotate images

  Python

  •

  MIT License

  •00 forks in CellProfiling/memento•11 star in CellProfiling/memento•00 issues in CellProfiling/memento•00 pull requests in CellProfiling/memento•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

  •11 fork in CellProfiling/2dShapeSpacePortable•11 star in CellProfiling/2dShapeSpacePortable•00 issues in CellProfiling/2dShapeSpacePortable•00 pull requests in CellProfiling/2dShapeSpacePortable•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

  •00 forks in CellProfiling/gui_for_wet_lab•11 star in CellProfiling/gui_for_wet_lab•00 issues in CellProfiling/gui_for_wet_lab•00 pull requests in CellProfiling/gui_for_wet_lab•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

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  GNU General Public License v3.0

  •00 forks in CellProfiling/HPA_Convert_OPERA_To_LIMS-OMETIF•00 stars in CellProfiling/HPA_Convert_OPERA_To_LIMS-OMETIF•11 issue in CellProfiling/HPA_Convert_OPERA_To_LIMS-OMETIF•00 pull requests in CellProfiling/HPA_Convert_OPERA_To_LIMS-OMETIF•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

  •11 fork in CellProfiling/HPA_SingleCellClassification_Analysis•22 stars in CellProfiling/HPA_SingleCellClassification_Analysis•00 issues in CellProfiling/HPA_SingleCellClassification_Analysis•00 pull requests in CellProfiling/HPA_SingleCellClassification_Analysis•Updated Feb 10, 2026Feb 10, 2026

• 2D_shapespace

  Public
  Jupyter Notebook

  •11 fork in CellProfiling/2D_shapespace•11 star in CellProfiling/2D_shapespace•00 issues in CellProfiling/2D_shapespace•00 pull requests in CellProfiling/2D_shapespace•Updated Feb 10, 2026Feb 10, 2026

• CAR-TCell-MPX-Analysis

  Public
  Python

  •

  MIT License

  •11 fork in CellProfiling/CAR-TCell-MPX-Analysis•11 star in CellProfiling/CAR-TCell-MPX-Analysis•00 issues in CellProfiling/CAR-TCell-MPX-Analysis•00 pull requests in CellProfiling/CAR-TCell-MPX-Analysis•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

  •00 forks in CellProfiling/TifCs_To_HPA-PNG-JPEG•00 stars in CellProfiling/TifCs_To_HPA-PNG-JPEG•00 issues in CellProfiling/TifCs_To_HPA-PNG-JPEG•00 pull requests in CellProfiling/TifCs_To_HPA-PNG-JPEG•Updated Dec 3, 2025Dec 3, 2025

• Biomni_MCP

  Public
  Python

  •00 forks in CellProfiling/Biomni_MCP•00 stars in CellProfiling/Biomni_MCP•00 issues in CellProfiling/Biomni_MCP•00 pull requests in CellProfiling/Biomni_MCP•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

  •00 forks in CellProfiling/Sp8-Lif_To_Memento•11 star in CellProfiling/Sp8-Lif_To_Memento•00 issues in CellProfiling/Sp8-Lif_To_Memento•00 pull requests in CellProfiling/Sp8-Lif_To_Memento•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

  •00 forks in CellProfiling/HPA_Cilia_Study_Code•33 stars in CellProfiling/HPA_Cilia_Study_Code•00 issues in CellProfiling/HPA_Cilia_Study_Code•00 pull requests in CellProfiling/HPA_Cilia_Study_Code•Updated Sep 23, 2025Sep 23, 2025

• Squid

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •5757 forks in CellProfiling/Squid•00 stars in CellProfiling/Squid•00 issues in CellProfiling/Squid•00 pull requests in CellProfiling/Squid•Updated Sep 10, 2025Sep 10, 2025

• image-stitcher

  Public
  stitching together 5D OME-zarr from an input folder of microscope acquisition images

  Python

  •66 forks in CellProfiling/image-stitcher•00 stars in CellProfiling/image-stitcher•00 issues in CellProfiling/image-stitcher•00 pull requests in CellProfiling/image-stitcher•Updated Sep 8, 2025Sep 8, 2025