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.