[ome-devel] Request for feature development for FIGURE - for discussion by the community

[Ilan Davis]

Dear OME developer community

We love OMERO-figure. It has become a central way we use OMERO and we believe it is an under appreciated tool that everyone should use for all their day to day imaging. We would like to see the OMERO team embracing this and putting a small amount of effort in getting it even better. Please please please put these request high up on a priority list…

Motivation
Figure was developed to make it possible to make figures for papers directly from OMERO and bypassing illustrator and the like.
However, for us it has enabled an unintended additional use that we believe is more significant. It allows every time a user has an imaging session on a microscope to summarise the typical result of that session. It also allows a systematic record of a medium scale screen, again summarising how the user thinks the data should be viewed. Viewing raw data from a screen is rather difficult in comparison. We have been using Zegami, as a visualisation tool that can organise and slice and dice the figures at scale using rich n-dimensional meta-data of our choice including bioinformatics.

The following are specific requests framed in general terms and have mostly been posted previously over an extended period by various members of my group and Micron in Oxford.  David Pinto, Josh Titlow, MK Thompson will be at the next OMERO meeting in Dundee and can discuss these points in more detail.

Development requests

1) Make some small improvements to Figure so it is sufficient for making figures for papers (other than drawing diagrams and plots). e.g. scalable text and better text labels. Does not have to be extensive and complex. Just one labelling approach that is good.

2) Create a hierarchy of folders housing figures so that figures can be organised in a sensible way over time, at scale.

3) Use some kind of tagging system, similar to Auto-tag (or repurpose the Auto-tag code) - extracting tags from the folder and figure names.

4) Allow batch export of figures from pull down menus as well as CLI. At the moment we are pulling the figures from json files using our own bespoke python scripts.

5) Allow more format of figure export especially .png

6) Ideally export metadata with the figures including the tags and automate publishing of figure collections through Zegami with metadata (via .png and csv files).

I welcome comments, clarifications, questions or counterpoints.

with best regards
Ilan
For transparency:
I am on the SAB of Zegami and on the SAB of OMERO-IDR

p.s.If you would like to know more about Zegami, please look up.  https://zegami.com/



____________________________________________________________________________
Prof. Ilan Davis   ilan.davis at bioch.ox.ac.uk<mailto:ilan.davis at bioch.ox.ac.uk>   http://www.ilandavis.com
https://twitter.com/ilandavis
Department of Biochemistry, The University of Oxford, South Parks Road, OXFORD OX1 3QU, UK
Direct Office No: (44) (0)1865 613265  Office Fax: (44) (0)1865 613340
Lab manager: Dr Darragh Ennis darragh.ennis at bioch.ox.ac.uk<mailto:darragh.ennis at bioch.ox.ac.uk> (44) (0)1865 613271 / 613272
PA:  jolanta.parkinson at bioch.ox.ac.uk<mailto:jolanta.parkinson at bioch.ox.ac.uk>  (44) (0)1865 613218
____________________________________________________________________________








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