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    68 repositories

    • HPA_SingleCellClassification_Analysis

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

    • 2D_shapespace

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

    • cam_acq

      Public
      Python project to control microscope through client-server program.
      Python
      •
      Apache License 2.0
      •0•5•1•5•Updated Feb 9, 2026Feb 9, 2026

    • subcell-embed

      Public
      Codebase for training the SubCell models
      Python
      •
      MIT License
      •3•18•0•0•Updated Feb 9, 2026Feb 9, 2026

    • SubCellPortable

      Public
      This is a convenient code wrapper to run Lundberg lab SubCell model in inference with your own images
      Python
      •
      MIT License
      •4•5•0•0•Updated Feb 4, 2026Feb 4, 2026

    • ellviewer

      Public
      Simple and configurable layered viewer, serverless and zero-code configurable
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jan 23, 2026Jan 23, 2026

    • CAR-TCell-MPX-Analysis

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

    • camacq-plugins

      Public
      Plugins for camacq
      Python
      •
      Apache License 2.0
      •0•0•0•7•Updated Jan 23, 2026Jan 23, 2026

    • seq2loc_benchmark

      Public
      Code for "A comprehensive benchmark of sequence-based subcellular localization predictors for human proteins"
      Jupyter Notebook
      •0•0•0•0•Updated Jan 17, 2026Jan 17, 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

    • ell_code_template

      Public
      Python
      •0•0•0•0•Updated Oct 24, 2025Oct 24, 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•0•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
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Sep 23, 2025Sep 23, 2025

    • HPA_Convert_Sp8_To_OMETIF

      Public
      Java
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Sep 16, 2025Sep 16, 2025

    • Squid

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •48•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

    • HPACellSegmentatorPortable

      Public
      Just a rework of the HPA Cell Segmentator repository that works with modern and simple python libraries
      Python
      •0•0•0•0•Updated Aug 26, 2025Aug 26, 2025

    • subcell-analysis

      Public
      Jupyter Notebook
      •
      MIT License
      •0•10•0•0•Updated Aug 18, 2025Aug 18, 2025

    • MetabolismManuscript

      Public
      custom code written for the analysis of the manuscript "Widespread enzyme expression variations underly diverse metabolic capacities within cell types"
      Python
      •0•0•0•0•Updated Jul 30, 2025Jul 30, 2025

    • 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 Jul 5, 2025Jul 5, 2025

    • pipex

      Public
      A pipeline to transform images into valuable analysis items
      Python
      •
      MIT License
      •2•18•1•0•Updated Jun 18, 2025Jun 18, 2025

    • bioe-postdoc-chalktalk

      Public
      Website for the BioE Postdoc Chalk Talk
      HTML
      •0•0•0•1•Updated Feb 17, 2025Feb 17, 2025

    • covid19ai.io

      Public
      COVID19AI.IO -- An AI Model Repository for Fighting COVID-19
      Python
      •1•0•3•1•Updated Sep 3, 2024Sep 3, 2024

    • stable-diffusion

      Public
      A latent text-to-image diffusion model
      Jupyter Notebook
      •
      Other
      •11k•1•0•0•Updated Jun 24, 2024Jun 24, 2024

    • HDCA-FetalLung-SpatialProteomics

      Public
      Custom software written for analysis of spatial proteomics data from fetal lung acquired in the HDCA project.
      spatial-proteomicscell-atlasimagej-macroshuman-development-dataset
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jun 14, 2024Jun 14, 2024

    • lmc_GenCellPaint

      Public
      First place algorithm in ISBI 2024 Light My Cell competition, label-free cell painting
      Python
      •
      Other
      •4•0•0•0•Updated Jun 3, 2024Jun 3, 2024

    • CellCyclePlottingDataframes

      Public
      Dataframes for plotting the cell cycle data
      0•0•0•0•Updated May 13, 2024May 13, 2024

    • cpias

      Public
      :herb: Cell Profiling Image Analysis Server
      Python
      •
      Apache License 2.0
      •0•0•0•1•Updated Mar 20, 2024Mar 20, 2024

    • cell-pro-template

      Public template
      This repository serves only as a Python template for new projects
      Python
      •
      Apache License 2.0
      •1•0•0•1•Updated Mar 20, 2024Mar 20, 2024