Automated smFISH quantification for C. elegans embryos

Author: Naly Torres, PhD candidate

Erin O. Nishimura's Lab at Colorado State University

Collaborators: Luis de Lira Aguilera PhD

(October 6th, 2024) This repo is currently being edited: If you are interested or have questions please email: [email protected]

Description

Software to analyze smFISH images of C. elegans embryos in python. Requires non-deconvolved microscope images in organized subdirectories. Cell segmentation is performed using Cellpose and spot detection using FISHquant. Output is a csv file with mRNA counts per embryo and a report with images of the spot detection and segmentaion masks.

Code overview

Cell segmentaion

Uses Cellpose

Spot detection

Save files as png in subdirectories Uses Python

Calculate colocalization with C. elegans feautures

mRNA-membrane colocalization

mRNA-p granules colocalization

mRNA-nuclei colocalization

mRNA-mRNA colocalization

Data analysis and visualization

Installation

Tip

Install Anaconda before installing this repository and all its dependencies.

• Create conda environment

# conda create --name ce-bigfish
conda create --name ce-bigfish --file ce-bigfish.yml

• Activate conda environment

conda activate ce-bigfish

• Clone git repository

git clone --depth 1 https://github.com/TorresNaly/ce-bigfish.git

Last edited Oct 1st, 2024.