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

[Alexandre Dufour]

Splendid! Thanks Doug.


On 31 Jul 2015, at 14:23, 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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