Repositories list

• autofish-analysis

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 20, 2026Feb 20, 2026

• autofish

  Public
  Python code to control automated iterative FISH system

  Python

  •

  MIT License

  •00 forks•55 stars•77 issues•00 pull requests•Updated Jan 29, 2026Jan 29, 2026

• pipeline_HOX_apiFISH

  Public
  Jupyter Notebook

  •

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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 12, 2025Nov 12, 2025

• rna2seg

  Public
  rna2seg

  Python

  •

  MIT License

  •22 forks•2222 stars•55 issues•00 pull requests•Updated May 15, 2025May 15, 2025

• ComSeg

  Public
  comseg

  Python

  •

  MIT License

  •44 forks•2424 stars•66 issues•00 pull requests•Updated Feb 6, 2025Feb 6, 2025

• tutorial_gene_selection

  Public
  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 28, 2024Feb 28, 2024

• big-fish

  Public
  Toolbox for the analysis of smFISH images.

  pattern-classificationsegmentationspatial-features+ 3

  pattern-classificationsegmentationspatial-featuressmfishspot-detectionrna-localization

  Python

  •

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

  •2424 forks•7575 stars•1717 issues•22 pull requests•Updated Oct 31, 2023Oct 31, 2023

• fq-segmentation

  Public
  Wrapper code for segmentation of cells and nuclei with Cellpose.

  segmentationnucleicellpose

  segmentationnucleicellpose

  Python

  •

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

  •22 forks•22 stars•22 issues•11 pull request•Updated Jul 19, 2023Jul 19, 2023

• fq-imjoy

  Public
  ImJoy plugins to run different smFISH analysis in a user-friendly setting.

  imjoyimjoy-pluginssmfish

  imjoyimjoy-pluginssmfish

  HTML

  •

  MIT License

  •22 forks•33 stars•1717 issues•00 pull requests•Updated Mar 8, 2023Mar 8, 2023

• sim-fish

  Public
  Toolbox to simulate smFISH images.

  Python

  •

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

  •11 fork•1010 stars•11 issue•00 pull requests•Updated Sep 5, 2022Sep 5, 2022

• big-fish-examples

  Public
  Notebooks to illustrate how BigFISH is working.

  Jupyter Notebook

  •

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

  •99 forks•1212 stars•55 issues•00 pull requests•Updated Sep 5, 2022Sep 5, 2022

• fish-quant.github.io

  Public
  Landing page for fish-quant organization.

  imjoyfish-quantbig-fish

  imjoyfish-quantbig-fish

  JavaScript

  •

  MIT License

  •11 fork•11 star•11 issue•00 pull requests•Updated Feb 21, 2022Feb 21, 2022

• fq-interactive-docs

  Public
  Interactive ImJoy docs

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 11, 2021Feb 11, 2021