Toolbox for the analysis of smFISH images.
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Oct 31, 2023 - Python
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smfish
Here are 7 public repositories matching this topic...
Comprehensive, efficient, and adaptable MATLAB toolkit for the Chemical Master Equation (CME): finite state projection (FSP), stochastic simulations, moment dynamics, parameter inference, Fisher information and experiment design for discrete stochastic processes, including single-cell gene expression data.
matlab modeling systems-biology markov-chain computational-biology gene-expression parameter-estimation bayesian-inference single-cell stochastic-processes sbml metropolis-hastings experimental-design stochastic-simulation fisher-information chemical-master-equation smfish finite-state-projection
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Nov 3, 2026 - MATLAB
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
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Mar 31, 2026 - R
ImJoy plugins to run different smFISH analysis in a user-friendly setting.
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Mar 8, 2023 - HTML
Software for smFISH quantification with graphical interface, thought to be easy to install and use.
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Aug 31, 2026 - Python
This repository contains the Python modules and scripts to reproduce the results in the paper "Catanach, Vo, Munsky. IJUQ 2020."
inference bayesian bayesian-inference mcmc markov-chain-monte-carlo sequential-monte-carlo single-cell-imaging chemical-master-equation multifidelity stochastic-reaction-networks smfish
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Jul 28, 2021 - Jupyter Notebook
Counting mRNA clusters and single molecules in smFISH microscopy images. Two pipelines (STED clustering, confocal copy-number calibration), validated against synthetic ground truth.
python single-molecule image-analysis fluorescence microscopy cell-biology bioimage-analysis sted smfish
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Nov 1, 2026 - Python
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