We are doing a lot of high-throughtput IF analysis of ionizing radiation induced foci and we are trying to adapt QuPath to work with our workflow. Indeed, we are very satisfied with the current results. We are using Subcellular detection within the Cell Detection module to analyze IR induced foci in the nuclei of irradiated cells.
For small datasets we use Export Measurements to export the data of interest, but with large file number this does not work very efficiently. Therefore, we have generated a script to export the data:
def name = getProjectEntry().getImageName() + ‘.tsv’
def path = buildFilePath(PROJECT_BASE_DIR, ‘Results’)
path = buildFilePath(path, name)
saveDetectionMeasurements(path, ‘Nucleus: AF633 sum’, ‘Nucleus: AF488 sum’, ‘Nucleus: DAPI sum’, ‘Subcellular: Channel 2: Num Single Spots’)
print 'Results exported to ’ + path
print ‘!!! DONE !!!’
In many cases “saveDetectionMeasurements” or “saveAnnotationMeasurements” work great.
However, is there similar commands for saving Cell Detection measurements, as there are unexpected formating issues, for the ‘Subcellular: Channel 2: Num Single Spots’ routine?
Thank you in advance.