[ome-users] CZI dimension

Thu Feb 27 01:23:07 GMT 2014

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
> 