[ome-users] Issue when reading czi lines scans

Balaji Ramalingam (Staff) b.ramalingam at dundee.ac.uk
Tue Mar 22 11:38:06 GMT 2016


Thank you reporting your issue.
We were able to reproduce the issue locally.
A ticket has been filed on this regard,

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.


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


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.

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
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