[ome-users] AxioScan.Z1 *.czi fails to open

[Balaji Ramalingam (Staff)]

Hi Kai,


Thank you for reporting your issue and for submitting your files.

We were able to reproduce the issue using Bio-Formats 5.3.3 on FIJI.


I have filed a ticket on this regard,

https://trac.openmicroscopy.org/ome/ticket/13320#ticket


This will get looked into at the earliest.

I have also added you to the CC list and you will get notified when there

is a status change on the ticket.


Hope that helps.


Best,

Balaji

__________________

Mr Balaji Ramalingam

Software Developer

OME Team

School of Life Sciences

University of Dundee

From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Manuel Stritt <manuel.stritt at actelion.com<mailto:manuel.stritt at actelion.com>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Friday, 10 February 2017 at 07:50
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] AxioScan.Z1 *.czi fails to open

Hi Curtis,

it seems that the ZeissCZIReader gets stuck in the initFile() method in the
for (int i=0; i<planes.size(); i++) { ... loop.
For this file plane.size() is 681...

Regards,
Manuel




On Thu, Feb 9, 2017 at 6:01 PM, Curtis Rueden <ctrueden at wisc.edu<mailto:ctrueden at wisc.edu>> wrote:
Hi Kai,

You can find out what ImageJ is stuck doing by following these directions:

http://imagej.net/Troubleshooting#If_ImageJ_freezes_or_hangs

The stack trace will help the Bio-Formats developers to understand and fix the problem. Although in this case, since you uploaded sample data, that is probably already enough to reproduce.

Thanks,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Feb 9, 2017 at 10:39 AM, Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>> wrote:
Hi,

I have a Bright-field *.czi image containing 4 scenes/scopes (upload ID 17539) from the Zeiss Axioscan Z1 slidescanner that fails to open without error message (FIJI, latest Bio-Formats). FIJI is stuck during "Analysing...".

Manuel Stritt(Orbit) has reproduced the problem with some further insight:

tested with Bioformats 5.3.2:
IFormatReader reader = new ImageReader();
reader.setId("2017_02_03_12wksWTQm3179.czi");
reader.close();

hangs at reader.setId...

it seems that ZeissCZIReader gets stuck at initFile().

Notably, when I split the 4 scenes into 4 individual files they open fine.

Do you have an idea what the problem could be in this case?

Thanks for your help and cheers,
Kai

--
Please note my NEW PHONE NUMBERS: +41 61 207 57 31<tel:%2B41%2061%20207%2057%2031> (direct) +41 61 207 22 50<tel:%2B41%2061%20207%2022%2050> (central)<<
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
Phone: +41 61 207 57 31<tel:%2B41%2061%20207%2057%2031> (direct) +41 61 207 22 50<tel:%2B41%2061%20207%2022%2050> (central) | kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch>

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