Open Microscopy Environment

I have just been sent a DICOM format slide scan by Leica as a possible alternative to using the .scn formt (see http://www.openmicroscopy.org/community/viewtopic.php?f=13&t=1104).

This .zip file contains a top-level directory and a DICOMDIR file. The top-level directory contains various sub-directories, each of which contains a different number of files. I don't seem to be able to open up the whole set ('java.io.EOFException: Attempting to read beyond end of file.' if I try to open the DICOMDIR file) but I can open individual files using the ImageJ Bio-formats import and they seem to contain the sort of information from which I could create a pyramidal/zoomable slide....however, I'm not sure how I would go about this. Any ideas?

BW

Damion

Hi Damion,

I have just been sent a DICOM format slide scan by Leica as a possible alternative to using the .scn formt (see viewtopic.php?f=13&t=1104).

This .zip file contains a top-level directory and a DICOMDIR file. The top-level directory contains various sub-directories, each of which contains a different number of files. I don't seem to be able to open up the whole set ('java.io.EOFException: Attempting to read beyond end of file.' if I try to open the DICOMDIR file) but I can open individual files using the ImageJ Bio-formats import and they seem to contain the sort of information from which I could create a pyramidal/zoomable slide....however, I'm not sure how I would go about this. Any ideas?

The best thing to do would be to send us the .zip file - at the very least, there is a bug that we need to fix in Bio-Formats, and it may be that we can just update the DICOM reader to build the slide as well.

I think I have sent you information on how to send files to us previously, but if not (and you need somewhere to upload the file) then please let me know.

Regards,
-Melissa