Export Cell Detection measurements

Dear All,
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’)
mkdirs(path)
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.

Hi @emil.mladenov,

Could you please elaborate on where/how the Measurement exporter falls short? I would have thought it to be the best option here, as it can also export Cell measurements.
If you need something more intricate than what the GUI can offer, you can also use the MeasurementExporter class via scripting, as described here.

Dear Melvingelbard,

Thank you for your rapid response.

Indeed, The Measurement Exporter is a perfect option when you have small number of files.

In my QuPath project usually there are many images/files to be analyzed and I would like to have the data for every single one separately.

If I would like to do this I need to use the Measurement exporter for every single file, which takes time.

If I use Measurement exporter and select all the images, the data is exported in one big single file, containing combined data for all the images.

If you do not include the Image name tag you are completely lost.

Thank you for your suggestion to use MeasurementExporter class in a scripting. I will definitely take a look.

Thank you again for your help.

Emil

1 Like