Simple ImageJ script for sparse RNA-FISH data analysis with increased throughput.

ThunderFISH is a procedure developed for transcript counting in mouse embryonic stem cells for genes expressed at relatively low levels (<60mRNAs per cell). It allows imaging and analysis of up to 10,000 cells at high magnification a day.

ThunderFISH is a pre-processing tool that extracts 2D single-cell RNA-FISH images from your 3D microscopy images of large field of view (e.g. 100um x 100um). Such images are compatible with diffraction-limited spot counting provided by ImageJ plugin ThunderSTORM.

Detailed Manual containing i) sample preparation protocol, ii) introduction to how to use the ThunderFISH ImageJ script on test data.

Download the test data and follow the instruction in the manual (.pdf file) to perform ThunderFISH analysis.

https://drive.google.com/open?id=1Mi4qL1LLaGeOzjwV3k-8RKoDIH0qZpJG - folder containing test data

Dobrinic P, Szczurek AT, Klose RJ, 2021, PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency - https://www.nature.com/articles/s41594-021-00661-y (ThunderFISH charcterisation and comparison to other spot counting techniques can be found in the supplementary materials)