[ome-devel] Scottish Dental Education Online (SDEO) and Educational Virtual Microscopy

[William Moore]

Hi Luca,

It would be good to discuss options for building a web ROI editor.
This has been a missing feature of OMERO web client for a long time now.

Unfortunately when I last looked, I didn't find any nice libraries to provide simple drawing functionality.
This is a bit surprising given how useful this would be in a number of web apps.
So it may be necessary to build this "from scratch", E.g. using Raphael.js (as we use that for the current ROI display in web).

I have started to explore this option as part of OMERO.figure (see https://github.com/will-moore/figure/issues/79)
using Raphael.js and Backbone.js as in the existing figure app.

If this is successful, then I would hope that it provides something that can be reused in the web-client.
Either to reuse the code directly, or at least benefit from the experience! 
I'll keep you up to date on progress.

If you build an ROI editor as part of a Moodle plugin, is it possible to reuse this outside of Moodle?
What sort of timescale are you thinking of?
Any particular javascript libraries that you think might be useful for this?

 Regards,

  Will.



On 13 May 2015, at 16:15, Luca Lianas <luca.lianas at crs4.it> wrote:

> Hi Doug (and OME team, of course),
> we are facing a situation similar to the one described by Doug, in fact we are working on an integrated  system based on Moodle and OMERO the context of an European project on cytology training.
> 
> Our first goal, as stated above, is to have a complete integration with Moodle, but we are working to make possible to integrate OMERO.web with third-party software to provide a standard mechanism to interact with the web viewer using external Javascript code.
> The first development phase will be focused on enabling OMERO.web's javascript client to interact with third-part software, the second phase will be focused on the development of a prototype of a web editor for OMERO's ROIs so that it will be possible to define new regions of interest from the web client or from an external system (by using proper tools, of course).
> 
> We already started by adding a feature that enables users to select which ROIs will be shown on screen when using the web client
> 
> https://github.com/openmicroscopy/openmicroscopy/pull/3432
> 
> ROIs can be turned ON\OFF by using OMERO.web controls (since version 5.1.0) or by Javascript software as you can see from the example
> 
> https://github.com/lucalianas/openmicroscopy/blob/develop/examples/Web/embed_rois_selection.html
> 
> Our second task will be focused on adding a way to "inject" new ROIs to the web viewer.
> The idea is to make possible to create ROIs using an external system (calculate them using a script, draw them using a custom editor and so on...) and push them directly on the web viewer without saving these new items in OMERO's database (which means that external ROIs’ persistence will be managed by the third-part software).
> The only requirement is that these new ROIs must be passed to the viewer using the same specifications described for OMERO's "real" ROIs
> 
> https://www.openmicroscopy.org/site/support/ome-model/developers/roi.html
> 
> The third task will be the actual implementation of a web editor for OMERO’s ROIs, this editor could become a first prototype for the “real” editor in OMERO.web (of course, with the approval of the OME team :) ).
> 
> Right now we are focusing on integrating OMERO and Moodle by building a dedicated Moodle plugin. The teacher will be able to use ROIs defined within OMERO and his own ROIs that will be stored in Moodle's databases and pushed to the web viewer when needed. A ROI editor will be built as a part of Moodle's plugin (and will become a prototype for OMERO.web's ROI editor), this editor will be used both by the teacher (to build ROIs) and by students during exam session (they will be able to answer to some questions by drawing new regions or applying marks on an image, like dots or circles). Moodle plugin will be also used to display slides during lectures that will embed images stored within an OMERO server with the chance to turn ON\OFF specific ROIs during the lecture.
> 
> We are going to keep all of you informed on the various stages of the project (and I’m going to push some code to the OME repository).
> 
> Cheers
> 
> Luca
> 
> ---
> 
> Luca Lianas
> Data Fusion - Distributed Computing
> CRS4 - Centro di Ricerche, Sviluppo e Studi Superiori della Sardegna
> POLARIS, Edificio 1, 09010 PULA (CA - Italy)
> 
> Phone: 070/9250266
> Email: luca.lianas at crs4.it
> 
> 
>> On 22 Apr 2015, at 12:11, Bean, Douglas <douglas.bean at abdn.ac.uk> wrote:
>> 
>> Hi OME team,
>>  
>> The following is a rough plan based on our meeting before Christmas (Ola, Gus, Jason, Carlos and me) about virtual microscopy for education for Scottish universities.
>>  
>> Our ultimate aim is to make educational virtual microscopy (EVM) available for teaching and learning across all Scottish universities. As this would be a rather large undertaking, I suggest for the time being to focus on integrating EVM into SDEO (Scottish Dental Education Online) e-learning resources and move on from there once established.
>>  
>> As I understand it, the steps we need to achieve this would be as follows;
>> 1.      Upload some slides (files) to the server space earmarked for SDEO. Assuming I’m correct about that space being available.
>> 2.      Import the existing annotations / ROIs for these slides. I’m guessing this will be on OME systems too, at least for the time being.
>> 3.      OME will supply some Javascript that will allow me to embed EVM into a webpage and display the content from stages 1 and 2. I will see if I can integrate this into our e-learning to create the activities we need. This should satisfy user story C, below.
>> 4.      Create account request page (similar solution like Dundee Demo server) for lecturers registered with SDEO. This still needs some finely grained definition I think, but would be a start on user story B.
>> 
>> Once we’ve done this it would probably be a good idea to discuss what we’ve got and how we move forward etc.
>>  
>> I see there being a few user stories / use cases;
>> A.     A lecturer (from any given institution) can present slides during their lecture.
>> B.     A lecturer (from any given institution) can annotate slides with their own ROIs.
>> C.     A student can use EVM in directed study (e-learning).
>> D.     A student can use EVM in directed study (lecture materials).
>> E.      A student can use EVM in undirected study, browsing the catalogue.
>> 
>> Please add / comment / suggest alterations.
>>  
>> Regards
>> Doug
>>  
>> Douglas Bean MSc | Software Developer | SDEO.ac.uk
>>  
>> Mon - Wed - Medi-CAL Unit | Room 0.036 | Polwarth Building | University of Aberdeen | Foresterhill | Aberdeen | AB25 2ZD
>> Tel (direct): +44 (0)1224 43-7033 | Tel (unit): +44 (0)1224 43-7032
>>  
>> Thurs - Fri – University of Aberdeen Dental School | Argyll House | Aberdeen | AB25 2ZR
>> Tel +44 (0)1224 5 59608
>>  
>> 
>> 
>> The University of Aberdeen is a charity registered in Scotland, No SC013683.
>> Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
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