Repositories list

• memento

  Public

  CellProfiling/memento’s past year of commit activity
  A simple tool for sharing and annotate images

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• ProtiCelli

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

  Python

  •66 forks•1414 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• subcell-embed

  Public

  CellProfiling/subcell-embed’s past year of commit activity
  Codebase for training the SubCell models

  Python

  •

  MIT License

  •33 forks•1919 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• camacq-plugins

  Public

  CellProfiling/camacq-plugins’s past year of commit activity
  Plugins for camacq

  Python

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•11 pull request•Updated Apr 19, 2026Apr 19, 2026

• cam_acq

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

  Python

  •

  Apache License 2.0

  •00 forks•55 stars•11 issue•00 pull requests•Updated Apr 19, 2026Apr 19, 2026

• ell_code_template

  Public

  CellProfiling/ell_code_template’s past year of commit activity
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• SubCellPortable

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

  Python

  •

  MIT License

  •55 forks•55 stars•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• gui_for_wet_lab

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

  HTML

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 3, 2026Apr 3, 2026

• HPA_Convert_OPERA_To_LIMS-OMETIF

  Public

  CellProfiling/HPA_Convert_OPERA_To_LIMS-OMETIF’s past year of commit activity
  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

  •00 forks•00 stars•11 issue•00 pull requests•Updated Mar 6, 2026Mar 6, 2026

• subcell-analysis

  Public
  Jupyter Notebook

  •

  MIT License

  •11 fork•1111 stars•00 issues•00 pull requests•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

  •11 fork•11 star•00 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• 2D_shapespace

  Public
  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• ellviewer

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

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 23, 2026Jan 23, 2026

• CAR-TCell-MPX-Analysis

  Public
  Python

  •

  MIT License

  •11 fork•11 star•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 3, 2025Dec 3, 2025

• Biomni_MCP

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•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•11 star•00 issues•00 pull requests•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•33 stars•00 issues•00 pull requests•Updated Sep 23, 2025Sep 23, 2025

• HPA_Convert_Sp8_To_OMETIF

  Public
  Java

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 16, 2025Sep 16, 2025

• Squid

  Public
  Python

  •

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

  •5252 forks•00 stars•00 issues•00 pull requests•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•00 stars•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 30, 2025Jul 30, 2025

• pipex

  Public
  A pipeline to transform images into valuable analysis items

  Python

  •

  MIT License

  •22 forks•1818 stars•11 issue•00 pull requests•Updated Jun 18, 2025Jun 18, 2025

• bioe-postdoc-chalktalk

  Public
  Website for the BioE Postdoc Chalk Talk

  HTML

  •00 forks•00 stars•00 issues•11 pull request•Updated Feb 17, 2025Feb 17, 2025

• covid19ai.io

  Public
  COVID19AI.IO -- An AI Model Repository for Fighting COVID-19

  Python

  •11 fork•00 stars•33 issues•11 pull request•Updated Sep 3, 2024Sep 3, 2024

• stable-diffusion

  Public
  A latent text-to-image diffusion model

  Jupyter Notebook

  •

  Other

  •11k11k forks•11 star•00 issues•00 pull requests•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

  •00 forks•22 stars•00 issues•00 pull requests•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

  •44 forks•00 stars•00 issues•00 pull requests•Updated Jun 3, 2024Jun 3, 2024