[ome-devel] Status of features and fixes

[Sebastien Besson (Staff)]

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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