[ome-users] Reading CZI series image returns empty image while all the metadata are ok

[Balaji Ramalingam (Staff)]

Hi Sebi,

Thank you for submitting your file.
We were able to reproduce the bug locally across all the recent versions of Bio-Formats: 5.0.8 to 5.1.3 (i.e. does not look like a regression).

A ticket has been created on this regard,
https://trac.openmicroscopy.org/ome/ticket/12993
And you have been added to the cc list.

We’re intending to have this resolved for the upcoming 5.1.4 release.
Notifications will be sent to your email id, when there is a status change on the ticket.

Best,
Balaji


__________________

Mr Balaji Ramalingam

Software Developer

OME Team

College of Life Sciences

University of Dundee

From: Sebastian Rhode <sebrhode at gmail.com<mailto:sebrhode at gmail.com>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Monday, 17 August 2015 09:13
To: "ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>" <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: [ome-users] Reading CZI series image returns empty image while all the metadata are ok

Hi guys,

I recently files a Fiji Bug regarding the BioFormats Importer, but did not get any response so far. So maybe you are not aware of it yet. The original bug entry can be found here:

 http://fiji.sc/cgi-bin/bugzilla/show_bug.cgi?id=1139

I attached the 3 screeshos to illustrate the problem.

Sebi


[cid:ii_idfn9adm0_14f3ab8008f20fc9]
​
[cid:ii_idfn9miu1_14f3ab83e3626001]
​
[cid:ii_idfna0bn2_14f3ab884c2970de]
​

Original Post on Bugzilla:


I downloaded today's version of Fiji and tried to open a CZI series file via BioFormats 5.1.3 (contains 8 series) as I did many time before. But when the window opens, where one can select which series to open, all the thumbnails are black (see screenshot).

The XML metadata see to be OK, but the resulting import image contains only zeros. This used to work before without any problems and as far as I remember it wasa even no problem with BF 5.1.3 some days ago...

The CZI image can be found here:

https://dl.dropboxusercontent.com/u/623476/Tiles1_CH%3D2_Z%3D3_T%3D2_B2_B4_SingleCZI.czi


The University of Dundee is a registered Scottish Charity, No: SC015096
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