DesignNotes for new RKColocal ImageJ Plugin

Welcome to the RKColocal wiki!

This is a place for us to gather our thoughts on design / layout of the new ImageJ(2) RKColocal plugin.

General Plugin Structure

INPUT: two images, same size (perhaps give user option to choose two channels?); 'other parameters'

PRE-PROCESSING: Costes Autothreshold (method from Coloc2), before Pearsons/Manders/others?; perhaps offer other thresholding methods as well (manual?)

COLOC ALGORITHMS: ICQ; KendallTauBRank; Manders; Costes-Pearsons; MTKT ...

BLOCK SHUFFLE to calculate P-VALUE

OUTPUT: calculated coloc measures (both with and without thresholding?); p-values

TO DO

Ellen

1. Continue to write MTKT test Op
2. Update AutoThreshold Op ... fix tests
3. Update Pearsons methods to optionally include threshold... also, rename as they are Costes methods...

Random Thoughts

1. Provide users opportunity to pre-process images... most importantly, Costes AutoThreshold method (as in Coloc2) before Pearsons and Manders calculations...
2. Include warnings... ex) did auto thresh method work, is Pearsons<thresholds close to zero? ex) intercept far from 0? ex) regression slope far from 1 (could cause numeral problems in auto threshold)?