[ome-users] CZI dimension

Thu Mar 6 08:56:03 GMT 2014

Hi Curtis,

Thanks. In addition, I should also thank the team for including support for ImSpectorPro (*.msr) files. I've had no problems (yet!) opening these files since upgrading to Bioformats 5.

Paul.
____________________
Dr. Paul Thomas, Manager,
The Henry Wellcome Laboratory for Cell Imaging,
Faculty of Science,
University of East Anglia,
Norwich Research Park,
Norwich,
NR4 7TJ,
United Kingdom.

e-mail: p.thomas at uea.ac.uk
Tel: +44-1603-592196
Fax: +44-1603-592250
Imaging web-site: https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab
Personal web-page: https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people

From: ctrueden.wisc at gmail.com [mailto:ctrueden.wisc at gmail.com] On Behalf Of Curtis Rueden
Sent: 05 March 2014 20:08
To: Paul Thomas (SCI)
Cc: melissa at glencoesoftware.com; vbindokas; ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] CZI dimension

Hi Paul,

> I had to do a complete reinstallation of Fiji to update Bioformats to version 5.

I completed the update of Fiji to use Bio-Formats 5 earlier today. Simply updating Fiji should now give you a working Bio-Formats 5.0.0. And enabling the Bio-Formats update site (http://fiji.sc/Bio-Formats#Daily_builds) should give you the latest development builds.

Regards,
Curtis

On Thu, Feb 27, 2014 at 10:11 AM, Paul Thomas (SCI) <P.Thomas at uea.ac.uk<mailto:P.Thomas at uea.ac.uk>> wrote:
This didn't work for me, I had to do a complete reinstallation of Fiji to update Bioformats to version 5.
Paul.

____________________
Dr. Paul Thomas, Manager,
The Henry Wellcome Laboratory for Cell Imaging,
Faculty of Science,
University of East Anglia,
Norwich Research Park,
Norwich,
NR4 7TJ,
United Kingdom.

e-mail: p.thomas at uea.ac.uk<mailto:p.thomas at uea.ac.uk>
Tel: +44-1603-592196<tel:%2B44-1603-592196>
Fax: +44-1603-592250<tel:%2B44-1603-592250>
Imaging web-site: https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab
Personal web-page: https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people

> -----Original Message-----
> From: ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk> [mailto:ome-users-<mailto:ome-users->
> bounces at lists.openmicroscopy.org.uk<mailto:bounces at lists.openmicroscopy.org.uk>] On Behalf Of Melissa Linkert
> Sent: 27 February 2014 01:23
> To: vbindokas
> Cc: ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] CZI dimension
>
> Hi Vytas,
>
> > Might there be instructions on how to install the rc?  I did the
> > drag/drop in FIJI with bio-formats and/or loci_plugins jars [one at a
> > time], but when i ask help/about Loci, it still reports vers
> > 4.4.10-DEV. I take it I'm not running 5.0.
> > I've deleted all bio-formats and loci jars I found in fiji, except
> for
> > the installed rc.
> > What am I doing wrong?
>
> The best way to use 5.0.0 with Fiji is by following the instructions
> here:
>
> http://fiji.sc/Bio-Formats#Daily_builds
>
> Downloading the files by hand and copying them into the plugins folder
> is not recommended when using Fiji, as it is very easy to accidentally
> have an older version of the plugin still installed.
>
> If "Help > About Plugins > ..." shows something other than 5.0.0 after
> following those instructions, please let us know.
>
> Regards,
> -Melissa
>
> On Tue, Feb 25, 2014 at 09:27:04AM -0600, vbindokas wrote:
> > Dear Melissa,
> > Thanks for the response.
> > Might there be instructions on how to install the rc?  I did the
> > drag/drop in FIJI with bio-formats and/or loci_plugins jars [one at a
> > time], but when i ask help/about Loci, it still reports vers
> > 4.4.10-DEV. I take it I'm not running 5.0.
> > I've deleted all bio-formats and loci jars I found in fiji, except
> for
> > the installed rc.
> > What am I doing wrong?
> > thanks!
> >
> > On 2/24/2014 6:45 PM, Melissa Linkert wrote:
> > >Hi Vytas,
> > >
> > >>>It appears bioformats importer does not recognize the CZI fields
> > >>>created by the recent Lightsheet microscope system.  The
> lightsheet
> > >>>stored angular rotation "views" within the structure in addition
> to
> > >>>CH, T, Z. The importer does open the first 'view', but not beyond
> that.
> > >>>Can I request that tag/data be read for CZI?
> > >Which version of Bio-Formats are you currently using?  If you
> haven't
> > >already, I would suggest updating to 5.0.0-rc1:
> > >
> > >http://downloads.openmicroscopy.org/bio-formats/5.0.0-rc1
> > >
> > >and/or the very, very soon-to-be-released 5.0.0.  5.0.0-rc1 contains
> > >many improvements to .czi support, and I would expect it to open all
> > >rotations in a lightsheet dataset.
> > >
> > >>>The Zeiss software export is not very friendly [outputs views in
> > >>>stacks per Z and time], meaning that output must be then split and
> > >>>resorted to get data suitable for openSPIM processing.
> > >>>These are hugely big.
> > >>>If the czi could be opened as a virtual stack and then written out
> > >>>with the usual sequential tif naming, then it at least saves one
> > >>>step and much time/space.
> > >>>[I can try to upload a smaller czi file (5GBs), if that helps]
> > >A sample dataset would be very helpful if you find that there are
> > >still problems with 5.0.0-rc1/5.0.0.<http://5.0.0.>  If you are interested in
> > >uploading a file, please let me know and I will send the current FTP
> > >server information off-list.
> > >
> > >Regards,
> > >-Melissa
> > >
> > >On Fri, Feb 21, 2014 at 10:23:43AM -0600, Curtis Rueden wrote:
> > >>Hi Vytas,
> > >>
> > >>>It appears bioformats importer does not recognize the CZI fields
> > >>>created by the recent Lightsheet microscope system.
> > >>I am replying with the OME-users mailing list in CC, which is the
> > >>best place to report Bio-Formats issues.
> > >>
> > >>Regards,
> > >>Curtis
> > >>
> > >>
> > >>On Wed, Feb 19, 2014 at 8:45 AM, vbindokas
> <vbindoka at bsd.uchicago.edu<mailto:vbindoka at bsd.uchicago.edu>>wrote:
> > >>
> > >>>Dear Curtis,
> > >>>It appears bioformats importer does not recognize the CZI fields
> > >>>created by the recent Lightsheet microscope system.  The
> lightsheet
> > >>>stored angular rotation "views" within the structure in addition
> to
> > >>>CH, T, Z. The importer does open the first 'view', but not beyond
> that.
> > >>>Can I request that tag/data be read for CZI?
> > >>>The Zeiss software export is not very friendly [outputs views in
> > >>>stacks per Z and time], meaning that output must be then split and
> > >>>resorted to get data suitable for openSPIM processing.
> > >>>These are hugely big.
> > >>>If the czi could be opened as a virtual stack and then written out
> > >>>with the usual sequential tif naming, then it at least saves one
> > >>>step and much time/space.
> > >>>[I can try to upload a smaller czi file (5GBs), if that helps]
> best
> > >>>regards,
> > >>>
> > >>>--
> > >>>__
> > >>>
> > >>>Vytas Bindokas, Ph.D.
> > >>>Research Assoc. / Assoc. Prof.,
> > >>>Director, BSD Light Microscopy Core Facility
> > >>>phone: 773-702-4875<tel:773-702-4875>
> > >>>
> > >>>      [address for letters ONLY (see shipping addr below):] Dept
> > >>>Pharmacol Physiol Sci MC0926
> > >>>947 E 58th Street
> > >>>The University of Chicago
> > >>>Chicago IL 60637
> > >>>Room Abbott 129
> > >>>
> > >>>
> > >>>shipping address (main KCBD site):
> > >>>V. Bindokas
> > >>>900 E 57th Street
> > >>>KCBD room 1250, Microscopy Core
> > >>>The University of Chicago
> > >>>Chicago IL 60637
> > >>>
> > >>>
> > >>>email vbindoka at bsd.uchicago.edu<mailto:vbindoka at bsd.uchicago.edu>
> > >>>web site for LMCF:
> > >>>http://digital.uchicago.edu/index.html
> > >>>
> > >>>
> > >>_______________________________________________
> > >>ome-users mailing list
> > >>ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
> > >>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> > --
> > __
> >
> > Vytas Bindokas, Ph.D.
> > Research Assoc. / Assoc. Prof.,
> > Director, BSD Light Microscopy Core Facility
> > phone: 773-702-4875<tel:773-702-4875>
> >
> >      [address for letters ONLY (see shipping addr below):] Dept
> > Pharmacol Physiol Sci MC0926
> > 947 E 58th Street
> > The University of Chicago
> > Chicago IL 60637
> > Room Abbott 129
> >
> >
> > shipping address (main KCBD site):
> > V. Bindokas
> > 900 E 57th Street
> > KCBD room 1250, Microscopy Core
> > The University of Chicago
> > Chicago IL 60637
> >
> >
> > email vbindoka at bsd.uchicago.edu<mailto:vbindoka at bsd.uchicago.edu>
> > web site for LMCF:
> > http://digital.uchicago.edu/index.html
> >
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