[ome-users] [Bio-Formats] JPEG-XR via CZI

[Damir Sudar]

Hi Doug and all,
As an alternative to exporting/converting to tiff/bigtiff, is it an option
to turn off the JpegXR compression during acquisition and then use the
resulting czi files to import into OMERO or read with BioFormats?
Thanks,
- Damir

On Fri, Jul 31, 2015 at 5:23 AM, Doug Richardson <ds.richardson at gmail.com>
wrote:

> Hi Alexandre,
>
> If you update to ZEN2 it has much improved support for tif or bigtif
> export (both recognized by Fiji/Bioformats). Although it takes a very long
> time to open the largest files. During export we subset by scene and
> channel and this makes things manageable.
>
> If you don't have ZEN2 you can get the somewhat clunkier stand alone czi
> to tif converter. Linked from here on our website:
> http://hcbi.fas.harvard.edu/resources_software
>
> Zeiss should also be able to help you with this.
>
> Doug
>
>
>
> Sent from my iPhone
>
> On Jul 31, 2015, at 8:08 AM, Alexandre Dufour <adufour at pasteur.fr> wrote:
>
> Thanks for the prompt reply Josh.
>
> Just for my information: since it appears this isn’t going to be done
> anytime soon, and we do have a lot of users no this new machine, what
> alternative solution should I lean towards (in other words, what should I
> tell them)?
>
> Cheers
> Alexandre
>
>
> On 31 Jul 2015, at 14:06, Josh Moore <josh at glencoesoftware.com> wrote:
>
> On Fri, Jul 31, 2015 at 1:44 PM, Alexandre Dufour <adufour at pasteur.fr>
> wrote:
>
> Hi everyone,
>
>
> Hi Alexandre,
>
>
> I was trying to fiddle with a CZI file that has JPEG-XR compression, alas
> it
> won’t open via the latest Bio-Formats (official or nightly), with the
> following error:
>
> loci.formats.UnsupportedCompressionException: JPEG-XR not yet supported
>
> After digging through some archives, I found:
> - this ticket: https://trac.openmicroscopy.org/ome/ticket/8493
> - this PR: https://github.com/openmicroscopy/bioformats/pull/1014
> which suggests that the issue had been fixed over a year ago, hence my
> surprise.
>
>
> Sorry for the surprise. We did indeed start the work on a JPEG-XR
> codec but realized that we weren't going to be able to complete it and
> achieve our other goals. The PR you reference (8493) added as the
> title says the "initial structure" for the package, but the critical
> methods are not yet implemented. Similarly, all the JPEG-XR tickets
> (8493 and the 12 associated tasks) were all closed: "needsfunding"
> about 3 months ago:
>
>  Resolution set to needfunding
>  Status changed from accepted to closed
>
> We're certainly also interested in seeing this supported, but at the
> moment, no work is ongoing.
>
> All the best,
> ~Josh
>
>
>
> I have such a sample with me if you are interested (FTP access preferred).
>
> Cheers
> Alexandre
>
> —
> Alexandre Dufour, PhD
>
> Senior Research Fellow @ Biological Image Analysis group
> Institut Pasteur, Dpt. of Cell Biology & Infection, Paris campus (France)
> CNRS UMR 3691 “Pathological and Physiological Cell Dynamics”
>
> Meet Icy, the next-generation Bioimage Informatics platform
>
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-- 
Damir Sudar - Staff Scientist
Lawrence Berkeley Laboratory / Life Sciences Division
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov

Visiting Scientist, Oregon Health and Science University
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