Open Microscopy Environment

I am using “Bio-Formats” to open a 3-dimensional DICOM image in Fiji. The DICOM image is stored as 160 files (“0000.dcm” to “0159.dcm”), with one image slice in each file. Without problem, I can open an individual file (i.e. one slice), using Bio-Formats Import Options: Hyperstack, XYCZT, Open files individually, Color mode = Default, Autoscale.

However, when I uncheck the option “Open files individually,” in order to read the entire 160 slice image, the resulting image is defective: it appears to have treated the data as Little-Endian, when the data is actually Big-Endian. (It could be vice-versa, but the DICOM information says: “LittleEndian = false.”)

Working outside Fiji/ImageJ, the “RadiAnt DICOM Viewer” is able to read both an
individual *.dcm file, and the entire 160 slice image, without difficulty.

Hi

Could you upload your image: http://qa.openmicroscopy.org.uk/qa/upload/ and someone will take a look at it. Ideally see if you can reproduce the problem with a smaller image, if not just zip up and upload all planes.

Thanks, Simon