[ome-users] CZI dimension

Wed Mar 5 20:07:47 GMT 2014

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>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
> 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
>
> > -----Original Message-----
> > From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-
> > 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
> > 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.  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>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
> > > >>>
> > > >>>      [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
> > > >>>web site for LMCF:
> > > >>>http://digital.uchicago.edu/index.html
> > > >>>
> > > >>>
> > > >>_______________________________________________
> > > >>ome-users mailing list
> > > >>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
> > >
> > >      [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
> > > web site for LMCF:
> > > http://digital.uchicago.edu/index.html
> > >
> > _______________________________________________
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> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
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