Scripts to assess 3D confocal image warping towards a template image.

all run as:

python scriptname.py AlignedImage.nrrd Template.nrrd Results.csv

Results can be combined or sent to individual files and consist of:

Score, Methord, AlignedImage.nrrd,Template.nrrd

Analysis methords available are:

Overlap coefficient - OverlapCoeff.py

Pearson's coefficient - PearsonCoeff.py

Object Pearson's coefficient - ObjPearsonCoeff.py

Spearman coefficient - SpearmanCoeff.py

RMS difference - Quality.py

coefficient scores are all 1=perfect, 0=no correlation and with Pearson methords also returing -1 if anticorrelated.

RMSd returns a value that can only be compared when the same template is used. With 0 being bad and a good value range having to be experimentally estimated on the images used.