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

[Melissa Linkert]

Hi Carmine,

> 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.

Apologies for the delay.  We can now reproduce this problem, and are
testing a fix now:

https://github.com/openmicroscopy/bioformats/pull/2076

We anticipate that this fix will be included in the upcoming 5.1.6
release of Bio-Formats.

Regards,
-Melissa

On Fri, Oct 30, 2015 at 11:14:51AM +0000, Balaji Ramalingam (Staff) wrote:
> 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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