[ome-users] CZI dimension

[Melissa Linkert]

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
> >
> >

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