⚠

NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 868 - BF does not open some .stk file correctly
BF does not open some .stk file correctly
Status: RESOLVED WONTFIX
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
PC All
: P5 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-07-28 08:56 CDT by marelo64
Modified: 2014-07-29 07:59 CDT
1 user (show)

See Also:

Attachments
Contain file1.stk and file2.stk (1.28 MB, application/zip)
2014-07-28 08:56 CDT, marelo64

Description marelo64 2014-07-28 08:56:36 CDT 
Created attachment 185
Contain file1.stk and file2.stk

Note that I use a recent IJ/Fiji version (and the bug has also been noticed with an older IJ version few months ago).

Some .stk files are not correctly detected by BF and IJ open them with two axes (Z and T) while only one exist. Examples (axes order is T, Z, X, Y, C) :

- file1.stk : real shape = (10, 1, 264, 268, 1), BF detected shape = (5, 2, 264, 268, 1)

- file2.stk (with several channels): real shape = (10, 1, 139, 224, 3), BF detected shape = (5, 2, 139, 224, 3)

Both files have been saved from Metamorph after a z-projection (I bet the issue comes from here).

They open well on different Metamorph versions and also tifffile.py lib detects the correct shapes.

If you this place is not appropriate for this kind of bug, feel free to redirect me to the right place.

Both files are in the attachment file called stk_files.zip
Comment 1 Mark Hiner 2014-07-29 07:29:15 CDT 
How are you opening these files exactly? File > Open, or the Bio-Formats importer?
If you could test both of these methods and report back on the results, that would be very helpful.

Thanks,
Mark
Comment 2 marelo64 2014-07-29 07:31:11 CDT 
Sorry I forgot to mention that it's the same result with BF importer and File > Save. This is why I think it's related to BF readers.
Comment 3 Mark Hiner 2014-07-29 07:45:22 CDT 
No problem.. I thought that was what you meant, but wanted to confirm.

I agree with your assessment; it sounds like a bug in Bio-Formats itself.

So you'll have to bring this up with the Bio-Formats developers (OME team). Their guide for bug reporting is: http://www.openmicroscopy.org/site/support/bio-formats5/about/bug-reporting.html

You'll want to send an e-mail to the OME-Users mailing list: http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

They have their own ticketing system, so I'm going to close this issue for now. If it turns out that there this is related to a problem in Fiji we can reopen it.

Hope that helps,
Mark
Comment 4 marelo64 2014-07-29 07:59:38 CDT 
Perfect. I'll do that.