Random bug on opening CZI file: deformed image

[amichaut]

I have data acquired with Zen Blue. They are multi positions tiles. I stitched and fused the data with Zen and then open the data with BioFormats on Fiji. Some of the positions open fine and some are completely stretched, while everything looked fine on Zen. See screenshot, the image on the left is wrong, while the one the right is fine. They are two positions from the same file.
The same positions have the same issue on different computers (on Debian Jessie and on Mac OSX 10.11)
Has someone already encountered this problem?
Thanks!

[mlinkert]

Could you please confirm which version of Bio-Formats is installed in Fiji? "Help > About Plugins > Bio-Formats Plugins" will show the version number; if you see something other than 5.1.9 or 5.1.0, then please first try updating.

If you see the same problem with 5.1.9 or 5.1.0, then would you be willing to upload the problematic file so that we can investigate further? If so, files smaller than 2GB can be uploaded to:

https://www.openmicroscopy.org/qa2/qa/upload/

If the file is larger than 2GB, let us know and we will provide an alternate upload method.

[amichaut]

I am running the last release 5.1.9.
I uploaded a file. Series 1 and 2 are okay and the bug happens on series 3

[amichaut]

An additional piece of information (and possible work around): the bug does not appear if the different tiles are split in different files with the Zen software.

[bramalingam]

Hi,

Thank you for submitting your data,
We are currently reviewing the same locally and will get back to you with more information on the same, at the earliest.

Best,
Balaji

[jburel]

Thanks again for uploading the data
I can see the issue you mentioned on the 3rd series only.
The "line" only seems to appear in the first channel, the second channel seems to match the screenshot you posted above.
I will create a trac ticket. Do you wish to be cc'd?

Regards
Jmarie

[amichaut]

Yes it appears only on some series (that's why I called it random bug).
I found a work around (by splitting the series on ZEN software before opening individual series with bioformats), but yes I'd like to be cc'd.
Many thanks

[bramalingam]

Hi,

Thank you for your patience.
We were able to reproduce the issue and a ticket has been filed on this regard,
https://trac.openmicroscopy.org/ome/ticket/13233

and will get looked into at the earliest.
Please let us know if you would like to get added to the CC list on the ticket.

Best,
Balaji

[amichaut]

Thanks a lot. Yes I'd like to be cc'd.
Regards,
Arthur