Repositories list

• cam_acq

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

  Python

  •

  Apache License 2.0

  •0•5•1•0•Updated Jun 12, 2025Jun 12, 2025

• camacq-plugins

  Public
  Plugins for camacq

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jun 12, 2025Jun 12, 2025

• ell_code_template

  Public
  Python

  •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025

• pipex

  Public
  A pipeline to transform images into valuable analysis items

  Python

  •

  MIT License

  •2•13•2•0•Updated Jun 4, 2025Jun 4, 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•0•0•Updated May 29, 2025May 29, 2025

• SubCellPortable

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

  Python

  •

  MIT License

  •3•3•1•0•Updated May 16, 2025May 16, 2025

• 2D_shapespace

  Public
  Jupyter Notebook

  •1•0•0•0•Updated May 13, 2025May 13, 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 May 5, 2025May 5, 2025

• Squid

  Public
  Python

  •

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

  •39•0•0•1•Updated Apr 29, 2025Apr 29, 2025

• Sp8-Lif_To_Memento

  Public
  FIJI plugin that reads .lif files from the Sp8 confocal microscope and outputs a file system with pngs for Memento.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 26, 2025Apr 26, 2025

• subcell-analysis

  Public
  Jupyter Notebook

  •

  MIT License

  •0•5•0•0•Updated Apr 14, 2025Apr 14, 2025

• HPA_Convert_Sp8_To_OMETIF

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 7, 2025Mar 7, 2025

• bioe-postdoc-chalktalk

  Public
  Website for the BioE Postdoc Chalk Talk

  HTML

  •0•0•0•1•Updated Feb 17, 2025Feb 17, 2025

• subcell-embed

  Public
  Codebase for training the SubCell models

  Python

  •

  MIT License

  •3•13•0•0•Updated Feb 17, 2025Feb 17, 2025

• ellviewer

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

  HTML

  •

  MIT License

  •0•0•0•0•Updated Nov 11, 2024Nov 11, 2024

• 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 Nov 5, 2024Nov 5, 2024

• 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

  •10k•1•0•0•Updated Jun 24, 2024Jun 24, 2024

• 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 Jun 14, 2024Jun 14, 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+ 1human-development-dataset

  Jupyter Notebook

  •

  MIT License

  •0•2•0•0•Updated Jun 14, 2024Jun 14, 2024

• CellCyclePlottingDataframes

  Public
  Dataframes for plotting the cell cycle data

  0•0•0•0•Updated May 13, 2024May 13, 2024

• cpias

  Public
  🌿 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

• hpa_densenet

  Public
  Running the Bestfitting Densenet model

  Python

  •

  MIT License

  •2•0•0•4•Updated Mar 13, 2024Mar 13, 2024

• HPA-Cell-Segmentation

  Public
  Python

  •

  Apache License 2.0

  •26•95•0•0•Updated Jan 25, 2024Jan 25, 2024

• HPA_LIMS_Channel_Selector

  Public
  An ImageJ plugin to keep only the best channel from two channels, acquired under the same settings but with different gain or exposure times.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 27, 2023Dec 27, 2023

• FucciSingleCellSeqPipeline

  Public
  Cell cycle analysis of single-cell proteomic and transcriptomic data for the FUCCI cell model -- RNA-Seq analysis pipeline

  Python

  •4•7•1•0•Updated Oct 19, 2023Oct 19, 2023

• SingleCellProteogenomics

  Public
  Cell cycle analysis of single-cell proteomic and transcriptomic data for the FUCCI cell model

  Python

  •5•13•0•0•Updated Oct 19, 2023Oct 19, 2023

• HPA_SingleCellClassification_Analysis

  Public
  Analysis for Kaggle Human Protein Atlas Single Cell Classification challenge and 1st place solution

  Python

  •1•0•0•0•Updated Oct 18, 2023Oct 18, 2023

• memento

  Public
  A simple tool for sharing and annotate images

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 17, 2023Oct 17, 2023