Problems opening ZVI-files

Hi,

Is there any way of opening ZVI-files in CellProfiler 2.0? I can open TIF-files without problems, but with the ZVI-files I just get the error message that no files could be found.

cheers,
Karl-Johan

Hi Karl-Johan,

At this point, CellProfiler doesn’t support ZVI files although Bio-Formats (the package which we use for file format reading) supports them so this should be easily added. In the meantime, multiframe TIFs and STKs are supported, so if you are able to output your data in either of these forms, you should be able to work with them.

Regards,
-Mark

Hi,

Thanks for the reply. I managed to modify the code of LoadImages to also incorporate ZVI-files - as you said, it was actually quite easy once I understood the code structure. I just handled them in the same way flex-files are handled.

regards,
Karl-Johan

Cool! Would you mind posting the changed code?
-Mark

Of course. Here is the modified LoadImages file.
It seems to work for me; I can load multichannel Z-stacks from ZVI-files, which is what I wanted. However, I can’t guarantee that it’ll work for *all *kinds of ZVI-files… :smile:

regards,
Karl-Johan
loadimages.zip (28.8 KB)

Thanks!
I’ve patched loadimages.py, run unit tests, performed some arcane editing in upgrade_settings (has to be done if you change setting choice text) and checked in as svn rev 10420. BTW, loadimages is oft-modified, most of the other code looks better, glad you muddled through.

–Lee