Analysis of smFISH images!

FISH-quant

What kind of analysis can I do?Start FISH-quant in ImJoy

Features

FISH-quant was designed to help you in the analysis of smFISH images.

Python

Analysis is performed with Python.

Open source

Entire code hosted publically on GitHub.

Scalable

Modular workflow suited for high-content applications.

ImJoy

ImJoy plugins for user-friendly data processing.

Packages

We provide several packages for different analysis tasks and levels of experience. For a detailed description of FISH-quant, we invited you to read our paper.

  • The Python core analysis package big-fish allows you to custom build your own analysis pipeline. The Jupyter noteboook tutorials explain the different analysis modules. To get a first feeling, you can start them on binder (starting the remote server can take some time): Binder
  • If you have no programming experience, we provide a user interface powered by ImJoy to perform standard smFISH analysis including segmentation, detection of individual and clustered RNA and post-processing. For a first taste, we invite you to check out our interactive documentation here.

big-fish

Python core analysis package with Jupyter notebook demos.

fq-imjoy

ImJoy plugins for the most common smFISH analysis workflow.

fq-segmentation

Deep-learning based cell/nuclei segmentation of with Cellpose & Imjoy.

sim-fish

Simulation of smFISH images and spot localization patterns.

Blog

Some milestones for FISH-quant.

  • 2021-cornes-et-al

    January 2022

    Developmental Cell paper

    We contributed a FISH-quant analysis to a study looking at transcriptional silencing in C. elegans Developmental Cell.

  • 2021-fq-paper

    March 2021

    FISH-quant paper

    Our paper describing FISH-quant is available on Bioarxiv.

  • 2021-nat-comm-paper

    March 2021

    Nature Comm paper

    Our paper studying local translation at centrosomes was published in Nature Communications.

  • 2020-dev-cell-paper

    September 2020

    Developmental Cell paper

    Our paper linking RNA localization and local translation is published in Developmental Cell. To get an overview, you can also read the nice preview from Chin & Lecuyer.

  • 2019:
    first line of
    big-fish

Development team

We are a team of mathematiciana, biophysicist and computer scientists.

Arthur IMBERT

Lead Developer

Florian MUELLER

Project supervision, Developer

Thomas WALTER

Project supervision, Developer

Wei OUYANG

Developer

Contact Us

If you encounter a bug or you have a suggestion for an improvement, please file a GitHub issue in the respective repository.

For any other question, don’t hesitate to contact us by email

Florian Mueller: muellerf.reserach@gmail.com

Arthur Imbert: arthur.imbert@mines-paristech.fr

Thomas Walter: thomas.walter@mines-paristech.fr