I do not know

Two workflows are proposed here:

one based on fiducials, the other one on cross-correlation.

Matlab toolbox to analyze single molecule mRNA FISH data. Allows counting the number of mature and nascent transcripts in 3D images. See 2513. Following toolboxes are required: - Optimization toolbox - Statistics toolbox - Image processing toolbox - (Optional) Parallel processing toolbox

Input data type: 3D image

Output data type: CSV

(from the webpage) >This usage example shows how to produce two-color images from spectrally unmixed data sets. It was written for an Alexa647/Alexa700 measurement on the Würzburg 1 biplane setup as documented in [Aufmkolk2012]. The first two tasks in this example produce prerequisite knowledge for the image generation, the alignment information (Produce linear alignment matrix) and the F2 ratios, i.e. the relative intensity of fluorophores between the channels. [Aufmkolk2012] Hochauflösende Mehrfarben-Fluoeszenzmikroskopie. Sarah Aufmkolk. Julius-Maximilians-Universität Würzburg. 2012-mar.

The ImageJ pligin, called PixFRET, allows a simple and rapid determination of channel bleed-through parameters and the display of normalized FRET images. see 2521

Input data type: 

Stacks with 2 channels (controls for bleed-through calculation) or 3 channels (FRET calculation)

Output data type: 

One Image with FRET values and One image with normalized FRET values