Open Microscopy Environment

Greetings,

I'm trying to open a .czi file created with Zen Blue with bfOpen.m for matlab and the newest stable loci_tools.jar. The pixel values for all the slices are empty (a big array of zeros). Upon further inspection, with the call of ChannelSeperator.openBytes(<plane>) the java application returns an array of zeros, instead of the the pixel values for that plane. Opening the file in the Zen Blue software shows signal on all slices.

Am I missing something here, or does loci_tools not support .czi images made with Zen Blue?

The particular image is available for download here: https://docs.google.com/open?id=0B2tsfjLgpFVhNjB1QXNCVTg4dkU

Busted out the source code, and got down to ZeissCZIReader.java (of course), but not much further. May have something to do with the variable planes not being correctly instantiated.

Thank you for reporting this problem, and for making an example file available.

The issue is that this file uses an unsupported type of compression, which is specific to the type of camera which was used to acquire the data. I have filed a ticket on our issue tracking system to add support for this:

https://trac.openmicroscopy.org.uk/ome/ticket/9398

If you wish to receive an automated email each time we update the status of that ticket, please let me know and I will CC you.

As a temporary measure, simply re-saving the .czi file in Zen Blue should yield a file that can be read by Bio-Formats (the only difference will be the compression applied to the images).

Regards,
-Melissa

Has this been addressed at all? I downloaded the newest version of loci_tools.jar and am still experiencing the same problem.

One more ticket has been filed corresponding to the latest file that you have uploaded (QA issue 7405):

https://trac.openmicroscopy.org.uk/ome/ticket/11204

You were CC'd on that ticket, and so will receive an automated email any time the status is changed. We are actively working on the open .czi tickets, but do not yet have fixed builds.

Is there a beta-version of this code that I can use until a tested version becomes available?

Once the above-mentioned ticket is closed, you could try these builds:

http://hudson.openmicroscopy.org.uk/vie ... artifacts/

Please be aware that use of those builds is at your own risk, as they are not stable release builds. While the ticket is still open, unfortunately there won't be any builds worth trying.