[ome-users] Issue when reading czi lines scans

[Balaji Ramalingam (Staff)]

Hi,

The link to the ticket is getting redirected to another ticket,
Here's the corrected link,
https://trac.openmicroscopy.org/ome/ticket/13186

Best,
Balaji

__________________

Mr Balaji Ramalingam

Software Developer

OME Team

College of Life Sciences

University of Dundee

From: Balaji Ramalingam <b.ramalingam at dundee.ac.uk<mailto:b.ramalingam at dundee.ac.uk>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Tuesday, 22 March 2016 11:53
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] Issue when reading czi lines scans

Hi,

The link to the ticket is getting redirected to another ticket,
Here's the corrected link,

__________________

Mr Balaji Ramalingam

Software Developer

OME Team

College of Life Sciences

University of Dundee

From: Balaji Ramalingam <b.ramalingam at dundee.ac.uk<mailto:b.ramalingam at dundee.ac.uk>>
Date: Tuesday, 22 March 2016 11:38
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] Issue when reading czi lines scans

Hi,

Thank you reporting your issue.
We were able to reproduce the issue locally.
A ticket has been filed on this regard,
https://trac.openmicroscopy.org/ome/ticket/13186<https://trac.openmicroscopy.org/ome/ticket/13179>

And you have been added to the cc list.
Notifications will be sent to your email id, when there is a status change
on the ticket.

Hope that helps.
Best,
Balaji

__________________

Mr Balaji Ramalingam

Software Developer

OME Team

College of Life Sciences

University of Dundee

From: Ponti Aaron <aaron.ponti at bsse.ethz.ch<mailto:aaron.ponti at bsse.ethz.ch>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Friday, 18 March 2016 16:25
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] Issue when reading czi lines scans

Hi,

I attach two small line-scan z stacks Image1.czi and Image2.czi with following characteristics:

Image1 (read properly):
Two channels (green and red)
Actual Dimensions: x y z =512 1 80
Pixel size: x z= 0.208um 0.5um

Image2 (read incorrectly):
One channels (only red)
Actual Dimensions: x,y,z =512, 1, 240
Pixel size: x,z= 0.208um, 0.5um

Image1 can be read properly by bio-formats 5.1.8 (resulting in a 512 x 1 x 80 dataset). Image2.czi is read incorrectly, resulting in a 512 x 1 x 1 dataset instead of 512 x 1 x 240 (the z information is lost). The only obvious difference between the two files is the number of channels.

Thanks for looking into this.
a2

----
Dr. Aaron Ponti
Software and Data Management Engineer
Image Analysis Specialist
Single Cell Unit
Department of Biosystems Science and Engineering (D-BSSE)
ETH Zürich
Office 2.24
Mattenstrasse 26
4058 Basel, Switzerland
aaron.ponti at bsse.ethz.ch<mailto:aaron.ponti at bsse.ethz.ch>
+41 61 387 33 74

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

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