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

[Carmine Di Rienzo]

Ciao Melissa,

that's a wonderful news! There is absolutely no need to apologies.

thank you very much

ciao

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

2015-11-10 5:43 GMT+01:00 Melissa Linkert <melissa at glencoesoftware.com>:

> 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
>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
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