[ome-devel] Status of features and fixes

[Andrii Iudin]

Hi Sebastien,

Thank you for confirming the status of MRC and Spider changes. Currently 
we do not have the specifics of DM4 format, but we are looking into a 
way to provide you with such.

Best regards,
Andrii

On 31/01/2017 15:00, Sebastien Besson (Staff) wrote:
> Hi Andrii,
>
> Answering the Bio-Formats specifics:
> - for MRC and Spider, as you rightfully said, these changes are 
> already distributed in Bio-Formats 5.2.0 and later. This release also 
> included breaking model changes and is not distributed in the current 
> OMERO 5.2 line but these improvements will be available in OMERO 5.3.0
> - for the DM4 format, one of the major issues is that we have no 
> specification for this format. In order to support new modalities, we 
> need to collect more data samples and assess the amount of work 
> required to update Bio-Formats. If you or anyone else in the community 
> with expertise in this modality want to be involved in the 
> development, please let us know.
>
> Best,
> Sebastien
>
>> On 31 Jan 2017, at 13:19, Andrii Iudin <andrii at ebi.ac.uk 
>> <mailto:andrii at ebi.ac.uk>> wrote:
>>
>> Hi Will,
>>
>> Thanks for implementing the reversion into the OMERO, more reasons 
>> for us now to look forward to the 5.3.0 release!
>>
>> Best regards,
>> Andrii
>>
>> On 30/01/2017 16:06, William Moore (Staff) wrote:
>>> Hi Andrii,
>>>
>>> In 5.3.0, “reverse intensity” will be supported by the OMERO 
>>> rendering engine and
>>> by the clients: See web client PR 
>>> https://github.com/openmicroscopy/openmicroscopy/pull/4839
>>>
>>> The “reverse intensity” can be specified per-channel, and we also 
>>> support a look-up-table per-channel.
>>>
>>>  I’ll leave the detail of Bio-Formats tickets to a Bio-Formats dev, 
>>> but can tell you that Bio-Formats 5.2.0 will be in OMERO 5.3.0 in March.
>>>
>>>  Regards,
>>>
>>>    Will.
>>>
>>>
>>>> On 30 Jan 2017, at 10:05, Andrii Iudin <andrii at ebi.ac.uk 
>>>> <mailto:andrii at ebi.ac.uk>> wrote:
>>>>
>>>> Dear OMERO Developers,
>>>>
>>>> With the release of 5.3.0 update approaching, I was wondering if 
>>>> you might, please, tell what is the status of the following 
>>>> features/fixes?
>>>> - Color inversion API. Initially discussed with William Moore on 
>>>> 14-01-2016 in ome-devel:
>>>> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2016-January/003566.html
>>>>
>>>> We have been provided with a script to test, approved it and it has 
>>>> added to the requirements gathering for further rendering support. 
>>>> However, as far as I know it is not yet available?
>>>>
>>>>
>>>> - Support of EMPIAR files. There are three tickets for Bio-Formats:
>>>> https://trac.openmicroscopy.org/ome/ticket/13057 (Reg: dm4 files)
>>>> https://trac.openmicroscopy.org/ome/ticket/13058 (Reg: mrcs files)
>>>> https://trac.openmicroscopy.org/ome/ticket/13059 (Reg: Spider files)
>>>>
>>>> MRCS and Spider should be implemented in Bio-Formats 5.2.0. Which 
>>>> is currently not yet supported by OMERO (would be in the March 
>>>> release?).
>>>> But DM4 has been moved to an enhancement request list. Is this 
>>>> still planned to be implemented?
>>>>
>>>> Many thanks and best regards,
>>>> Andrii
>>>> _______________________________________________
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>>>> ome-devel at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>>
>>>
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