[ome-devel] Request for feature development for FIGURE - for discussion by the community
Ilan Davis
ilandavis at me.com
Tue May 22 21:45:02 BST 2018
Hi Jason
thanks. I guess I will answer this a bit philosophically or strategically,
We are developing this ourselves, but my strong feeling is that we cannot really do a proper job of creating very good tools in the way we are doing it by patching our way between two non intra-operable systems and also without getting into the guts of the OMERO code.
I also think it is wrong to think of our workflows as specialised ones for a particular one off purpose. They are workflows that should be adopted by virtually all cell biology labs that I know of. Have you surveyed how people are using OMERO in non-specialist labs?
The way I see it, and perhaps failing to explain it properly, is that what we are doing is creating a general purpose workflow that should be a next-generation way of dealing with data transparently within a team. The team and individuals can define a way to browse their data that contains implicit information in its organisation and metadata and collection of panels and choice of “typical data” that allow members of teams to understand each others data. It also allows users to accumulate over time a history of the meaning of their data, as they acquire it bit by bit. So my PhD students for example, essentially have their figures made for their thesis as they go along.
I realise it maybe hard to grasp what I am talking about, as this is a bit of a sociological / anthropological point. It is not a revolutionary scientific idea. It is a workflow that I think everyone should adopt as standard. I suspect that eventually this will be considered mandatory for data transparency and integrity. Just having a collection of raw data is good, but not sufficient.
Strategically, from the point of view of the OMERO project using a work flow of this sort, would make the whole project adoptable by everyone who does microscopy rather than just the more advanced users with particularly skilled staff.
I am convinced that the OMERO team can create a better work flow than we can for a base level method of making all data that everyone acquires (not only high content screens) transparent and understandable by anyone.
I will respond to Will’s helpful and useful comments separately, as they are much more specific.
Regards
ilan
ps As steve and I will not be there, perhaps you (and Will and Josh M) can schedule time with Josh and MK to go through the wokflow, the scripts (that Steve wrote and Josh modified) as well as see the cloud version of Zegami in operation. I think it is easier to understand my point above by just seeing examples.
____________________________________________________________________________
Prof. Ilan Davis 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 (44) (0)1865 613271 / 613272
PA: jolanta.parkinson at bioch.ox.ac.uk (44) (0)1865 613218
____________________________________________________________________________
> On 22 May 2018, at 19:30, Jason Swedlow (Staff) <j.r.swedlow at dundee.ac.uk> wrote:
>
> Hi Ilan
>
> My €$£0.02.
>
> We really appreciate all these comments. As you will have seen, we just released OMERO.figure 4.0, where we add support for “big” images (really large X-Y planes), which has been requested over and over again and required a lot of work to get right (or at least roughly so).
>
> The broader point of putting Figures under management in a serious way is a very important point. Your lab clearly has some very interesting workflows, and I look forward to hearing more about them at the upcoming Users Meeting. The whole point of an open project is people take technology in all sorts of ways that we won’t have thought of. As Will stated, a few of these are on the list, and several others are new ideas—so thank you!!!
>
> We’ll discuss at the upcoming Users meeting, take in more feedback, and come up with a plan for taking these forward.
>
> Huge thanks again.
>
> Cheers,
>
> Jason
>
>
> From: William Moore <W.Moore at dundee.ac.uk>
> Date: Tuesday, 22 May 2018 at 15:41
> To: OME Development <ome-devel at lists.openmicroscopy.org.uk>
> Cc: Jason Swedlow <j.r.swedlow at dundee.ac.uk>, Joshua Titlow <joshua.titlow at bioch.ox.ac.uk>, mkaythomp_gmail_com <mkaythomp at gmail.com>, Darragh Ennis <darragh.ennis at bioch.ox.ac.uk>, Richard Parton <richard.parton at bioch.ox.ac.uk>, David Susano Pinto <david.pinto at bioch.ox.ac.uk>
> Subject: Re: [ome-devel] Request for feature development for FIGURE - for discussion by the community
>
> Hi Illan, <>
>
> Thanks for the all the feedback.
> It’s great to hear that OMERO.figure is being so useful for you and to get a clear idea of what improvements are needed.
>
> I’ll respond to the various requests below in-line...
>
>> On 16 May 2018, at 16:30, Ilan Davis <ilan.davis at bioch.ox.ac.uk <mailto:ilan.davis at bioch.ox.ac.uk>> wrote:
>>
>> 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.
>
> We have an existing feature request for “Stand-alone labels” (labels that can be placed anywhere on the page) https://trello.com/c/wtu7IVuN/10-stand-alone-labels <https://trello.com/c/wtu7IVuN/10-stand-alone-labels>.
> Does this cover your needs or are there other improvements to the existing panel labels that you’d like to see?
> You can set font-sizes on labels already. Does “scalable text” include some other functionality or more flexible sizes?
>
>
>> 2) Create a hierarchy of folders housing figures so that figures can be organised in a sensible way over time, at scale.
>
> The folders feature request is listed at https://trello.com/c/LwAVYUjm/165-save-figures-in-folders <https://trello.com/c/LwAVYUjm/165-save-figures-in-folders> with some discussion as to options and timescale
> (which is currently limited by the OMERO model for Folders - so this needs to change first in OMERO).
>
>> 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.
>
> A tagging system would consist of 2 main features.
> - ‘Add Tags’ dialog/panel - similar to that in webclient, and/or extend Auto-Tag (if users have lots of tokens in their figure names).
> - Browse Tag hierarchy from within the figure app.
> This could be a fair bit of work to do this properly (e.g. webclient Tag dialog is quite complex, so is webtagging). If we had “folders for figures”, would you still want Tagging for figures? Do you need both?
> NB: currently webclient (or Tag-searcher) will not display Tagged File-Annotations (figures).
> Card created at https://trello.com/c/X2lvut2c/192-add-tags-to-figures-browse-by-tag <https://trello.com/c/X2lvut2c/192-add-tags-to-figures-browse-by-tag>
>
>
>> 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.
>
> Batch export of Figures was previously being discussed at https://github.com/ome/omero-figure/issues/151 <https://github.com/ome/omero-figure/issues/151> (Josh Titlow).
> However, one of the main issues has been identified by David Pinto https://github.com/ome/omero-figure/issues/289 <https://github.com/ome/omero-figure/issues/289> which is the fact that the export creates a File Annotation on OMERO.
>
> We really need to split the Figure Export functionality out of the Figure_To_Pdf.py script so that we can generate figures directly from Python without requiring the scripting service. Some of that work was started at https://github.com/ome/omero-figure/pull/240 <https://github.com/ome/omero-figure/pull/240> to allow the web app to generate figures without the Scripting service. I abandoned this when it became clear that this wouldn’t work from the web, but it would still be useful in your case (and others) to allow batch exports etc.
>
>
>> 5) Allow more format of figure export especially .png
>
> PNG export should be quite straightforward to implement. Created card at https://trello.com/c/N0PQjMKJ/189-export-as-png <https://trello.com/c/N0PQjMKJ/189-export-as-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).
>
> Is there particular metadata other than Tags you’d like to export? Exporting an extra csv file would require export of a zip instead of PDF/TIFF, which would complicate
> the workflow a bit and we’d probably want to make it optional in that case.
> It may be that the best option here is to create a custom Python script that exports all the metadata you want in a format of your choice.
> This gives you the most flexibility and can be updated according to your needs without the UI and workflow changes for other users.
>
>
> Thanks again for your input.
>
> I look forward to more discussions at the OME meeting next week,
>
> Regards,
>
>
> Will.
>
>
> PS. Another release of OMERO.figure just went out today: http://www.openmicroscopy.org/2018/05/22/figure-4-0-0.html <http://www.openmicroscopy.org/2018/05/22/figure-4-0-0.html>
>
>
>>
>> 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/ <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 <http://www.ilandavis.com/>
>> https://twitter.com/ilandavis <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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