[ome-users] CZI dimension

[Curtis Rueden]

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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