Repositories list

• gui_for_wet_lab

  Public
  Simple GUI tools to for wet-lab experiment and sample preparation

  HTML

  •

  MIT License

  •0•1•0•0•Updated Mar 25, 2026Mar 25, 2026

• ell_code_template

  Public
  Python

  •0•0•0•0•Updated Mar 23, 2026Mar 23, 2026

• SubCellPortable

  Public
  This is a convenient code wrapper to run Lundberg lab SubCell model in inference with your own images

  Python

  •

  MIT License

  •5•5•0•0•Updated Mar 23, 2026Mar 23, 2026

• camacq-plugins

  Public
  Plugins for camacq

  Python

  •

  Apache License 2.0

  •0•0•0•1•Updated Mar 23, 2026Mar 23, 2026

• subcell-embed

  Public
  Codebase for training the SubCell models

  Python

  •

  MIT License

  •3•18•0•0•Updated Mar 23, 2026Mar 23, 2026

• cam_acq

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

  Python

  •

  Apache License 2.0

  •0•5•1•4•Updated Mar 22, 2026Mar 22, 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

• subcell-analysis

  Public
  Jupyter Notebook

  •

  MIT License

  •1•10•0•0•Updated Mar 2, 2026Mar 2, 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

• 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

  •1•1•0•0•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

• 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

• 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

  •51•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

• 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

• 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-macros+ 1

  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