melissalinkert
commented
5 years ago Looking into this a bit, I can't reproduce plane opening issues with the sample plate. A simple iteration over every plane:
import loci.formats.ImageReader;
public class Test {
public static void main(String[] args) throws Exception {
try (ImageReader reader = new ImageReader()) {
reader.setId(args[0]);
for (int s=0; s<reader.getSeriesCount(); s++) {
reader.setSeries(s);
for (int p=0; p<reader.getImageCount(); p++) {
/* debug */ System.out.println("opening plane " + p + " from series " + s);
reader.openBytes(p);
}
}
}
}
}opens 4 planes per series across all 9240 series without an exception. Is the sample plate the same as the one that was imported and is throwing exceptions?
Assuming not, my initial guess is that there is at least one truncated file, which we've encountered in other formats but don't thoroughly handle in ColumbusReader. https://github.com/openmicroscopy/bioformats/pull/3380 adds an extra check and relevant logging (which probably isn't a bad idea in any case), so that's at least something to try.
sbesson
While working on https://github.com/IDR/idr0056-stojic-lncrnas/pull/1, @dominikl reported failures while applying the rendering settings:
Looking at the stack trace server-side, the error is thrown while trying to access individual planes:
The reader allowing to read data exported from a PerkinElmer Columbus system was introduced specifically in the context of two IDR studies:
id0019andidr0020. As can be seen from the description or representative samples, the reader currently expects one file containing the pixel data (TIFF) per well samples.In the case of
idr0056, the dataset is structured such that all the well samples within one well are stored within a FLEX file. In order to be able to read the original submitted data, the reader needs to be updated to support this variant of the file format.Sample plate:
/uod/idr/filesets/idr0056-stojic-lncrnas/20190513-ftp/RNAi\ screenA/1921\[652\]/