Java program for counting fluorescent pollen tetrads

This program is for counting fluorescent pollen tetrads in three color intervals from fluorescently tagged lines (FTL) lines. The original description of these lines can be found here:

Francis KE, Lam SY, Harrison BD, Bey AL, Berchowitz LE and Copenhaver GP (2007) Pollen Tetrad-based Visual Assay for Meiotic Recombination in Arabidopsis. Proc. Natl. Acad. Sci.104: 3913-3918. doi:10.1073/pnas.0608936104

For a thorough description of experimental design and data collection, see the publication below. A description and image of the tetrad types (A-L) for three color intervals is also provided in this publication.

Berchowitz LE, Copenhaver GP (2008) Fluorescent Arabidopsis tetrads: A visual assay for quickly developing large crossover and crossover interference datasets. Nature Protocols 3(1): 41-50. doi:10.1038/nprot.2007.491

A tutorial on how to use the program is provided in the wiki (https://github.com/jmodlis/TetradAnalysis/wiki). The user is expected to either have three color image data (viewable in a program such as ImageJ/Fiji) from tetrads or to use the program as a tool for counting tetrads under a microscope.

Requires Java 1.8