[ome-users] Wrong data import for single point Airyscan from CZI file

[Balaji Ramalingam (Staff)]

Hi,

Thank you for submitting your files.
We are still in the process of verifying the issue, and it is taking us a little longer than expected.

We will get back to you at the earliest on this regard.

For future instances, it would be great if you could upload your files to our QA server,
https://www.openmicroscopy.org/qa2/qa/upload/

Best,
Balaji

__________________

Mr Balaji Ramalingam

Software Developer

OME Team

College of Life Sciences

University of Dundee

From: Carmine Di Rienzo <carmine.dirienzo at sns.it<mailto:carmine.dirienzo at sns.it>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Wednesday, 28 October 2015 12:43
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] Wrong data import for single point Airyscan from CZI file

Hi all,

since it is the first time for me writing in this mailing list, I want to get a chance to thank all of you for your contributing to this amazing and essential tools: without them my everyday lab work will not be the same.
Recently, I have been trying to import in Matlab by using bio-format tools a single point acquisition made by Zeiss LSM 880 with Airyscan and saved as CZI file. While the metadata are correctly read, the imported data contains only 0 and a couple of ones. Similar results can be obtained either by ImageJ or FIJI. Unfortunately, the problem has not been solved by updating bio-format tools and ImageJ/FIJI.
My OS is Window 7 and the java version is 8 update 65 (build 1.8.0_65-b17)

The original file (about 3GB), a sample of extracted data with Matlab, the script used, and a sample data extracted in ome.tiff by ZEN can be downloaded here<http://www.filemail.com/d/pkkpezusyphsqpr>. The archive password is attached to this email. Unfortunately, the link will expire in 7 days, please let me know if you need an updated one and I'll provide it immediately.

Any ideas and every suggestion will be really appreciated.

Thank you very much!

Carmine

--
Carmine Di Rienzo
PhD Student of Molecular Biophysics
Scuola Normale Superiore and
Center for Nanotechnology Innovation @NEST
Piazza San Silvestro 12
56127 Pisa, Italy

tel. +39-050-509124
fax. +39-050-509417
carmine.dirienzo at sns.it<mailto:carmine.dirienzo at sns.it>

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