Overview
The goal of this project is the migration of the FISH-quant software from MATLAB to python.
FISH-quant is a program written in Matlab for analyzing single molecule mRNA FISH data. It allows counting the number of mature and nascent transcripts in 3D images.
FISH-quant first detects and then localizes mature mRNA in three dimensions by fitting Gaussians to fluorescent spots; each mRNA then undergoes a quality test based on the measured point-spread function (PSF). This provides the three-dimensional (3D) position of mRNAs inside cells and the distribution of mRNA counts across the cell population.
The original FISH-quant is available at http://code.google.com/p/fish-quant/ with a detailed manual and test data.