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smRNA-FISH analysis from 'Enhancer control of transcriptional activity via modulation of burst frequency'

This repository contains all code used to analyse smRNA-FISH data from the project 'Enhancer control of transcriptional activity via modulation of burst frequency'.

Central steps involve:

  1. cell segmentation
  2. spot detection
  3. post-processing: assigning spots to cells, and check co-localisation

Repository Overview

  • docs: Contains all project documentation.
  • infrastructure: Contains detailed installation instructions for all required tools.
  • ipa: Contains all image-processing-and-analysis (ipa) scripts which are used for this project to generate final results.
  • runs: Contains all config files which were used as inputs to the scripts in ipa.
  • scratchpad: Contains everything that is nice to keep track of, but which is not used for any final results.

Setup

Detailed install instructions can be found in infrastructure/README.md.

Citation

Do not forget to cite our publication if you use any of our provided materials.