[ome-devel] Scottish Dental Education Online (SDEO) and Educational Virtual Microscopy
Luca Lianas
lucalianas at gmail.com
Fri Jul 3 11:00:42 BST 2015
Hi Will
sorry for the late answer.
I’m going to check the shape editor ASAP, I’m still working on the updates to OMERO.web UI to add a “standard” mechanism to interact with OMERO’s viewer from an external web system (our primary target is Moodle).
You can find what I’m working on at
https://github.com/lucalianas/openmicroscopy/tree/third_party_rois <https://github.com/lucalianas/openmicroscopy/tree/third_party_rois>
Check the methods to add external shapes, maybe they are what you need as well.
I still need to add a few things (a method to update shapes’ text and style and, of course, a “backup system” to restore them to their original form), document methods and I’ll push a new pull request to the main repository.
Cheers,
Luca
---
Luca Lianas
> On 01 Jul 2015, at 00:41, William Moore <will at lifesci.dundee.ac.uk> wrote:
>
> Hi Luca,
>
> You can see and try a first working prototype of my "shape-editor" at
> http://will-moore.github.io/shape-editor-js/ <http://will-moore.github.io/shape-editor-js/>
>
> Still need to implement zooming, and provide helper methods for adding shapes etc.
>
> Let me know any feedback or questions you have.
>
> Cheers,
>
> Will.
>
>
> On 8 Jun 2015, at 11:26, William Moore <will at lifesci.dundee.ac.uk <mailto:will at lifesci.dundee.ac.uk>> wrote:
>
>>
>> Hi Luca,
>>
>> I would like to update you with work I have been doing towards web ROI editing and summarise discussions I had with
>> Gianluigi in Paris.
>>
>> I have been working on a shape editing tool as part on OMERO.figure: https://github.com/will-moore/figure/pull/87 <https://github.com/will-moore/figure/pull/87>
>> (see screenshot there) which uses the Backbone.js library.
>> But after discussion in Paris, it seems to make more sense to develop a common shape-editing library (using Raphael)
>> that does not depend on Backbone.js, which can then be used in other places, such as your Moodle plugin and
>> within the OMERO webclient.
>>
>> We discussed various differences between how ROIs & shapes are currently displayed in Insight, webclient, ImageJ
>> and my OMERO.figure work above,
>> with a view to improve some of the issues that have been noted so far:
>>
>> - ROIs & Shapes:
>> The OMERO model has "Shapes" (e.g Rectangle, Line) that are grouped into "ROIs". However, there are times when we
>> will want to ignore ROIs and just draw shapes (OMERO.figure & Moodle plugin, so these will not be included in a
>> shape-editing library.
>>
>> - Fill colour:
>> OMERO shapes have a fill-colour, which is supported by both Insight and Web. However, this usually just obscures the
>> region that is annotated and is not required for image annotations. E.g. ImageJ has no fill colour and figures never show this.
>> Best to assume that shapes have no fill colour by default (could be added later if needed).
>>
>> - Line colour / selection:
>> OMERO.insight and web client use a blue line to indicate which shape is selected (along with display of handles in Insight).
>> However, this interferes with the current colour of the line, making it hard to tell when the colour is changed for a selected shape.
>> It should be sufficient to indicate the selected shape by simply displaying "handles" for editing. This is a common technique
>> - E.g. used in Powerpoint (and see OMERO.figure screenshot on PR above).
>>
>> - Zooming:
>> When you zoom the image in Insight, the line thickness of shapes changes accordingly but the handles remain a fixed size.
>> This behaviour should be followed in web too.
>> Any shape-editing tool will need a setZoom() function to update it as the image zooms.
>>
>> - Shape creation vv Editing:
>> Although we didn't discuss this in Paris, I have previously found that the behaviour in Insight when creating shapes to be a little
>> restrictive. E.g. when creating Rectangles, after you have drawn the first one, you can't tweak it before adding another, even though it has handles for editing.
>> I have tried to follow ImageJ behaviour for shape creation / editing, in which shapes become selected when added and can
>> be edited with the handles (or dragged). This also allows for adding multiple shapes in succession, as long as you don't try to add new shapes
>> entirely within the last-added shape (without de-selecting first).
>>
>>
>> I'll let you know when I've managed to make any more progress on this.
>>
>> Cheers,
>>
>> Will.
>>
>>
>>
>>
>> On 13 May 2015, at 16:15, Luca Lianas <luca.lianas at crs4.it <mailto: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 <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 <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 <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 <mailto:luca.lianas at crs4.it>
>>>
>>>
>>>> On 22 Apr 2015, at 12:11, Bean, Douglas <douglas.bean at abdn.ac.uk <mailto: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 <http://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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