3D Brain viewer and selection

Michaela wrote:

we are wondering whether there is any way to visualize this in 3D. Do you have an idea how to include the annotations in a real simulation? I know we didn't talk about 3D before, but maybe you have an idea how to easily include this as I am not familiar with all the TVB details yet. This would be an important step for us to show in addition to your screenshots where brain regions are depicted as squares only.

My answer

• About 3D
  I have considered the following options:
  • A - When the users selects one region of TVB in the 3D viewer on the left-side, immediately focus on the BRCO annotation on the right.
    This would be, in my opinion, a better alternative, to what we previously discussed: to include the BRCO annotation on the context menu of a node (which is appearing only on right click), as we have more space, and in modern UIs, the context menu is often considered deprecated as not too intuitive to use.
  • B - When a user goes with his mouse over the right-side (or clicks on the right-side in the BRCO tree), highlight with a different colour the corresponding TVB region on the left-side in 3D (see attached screenshot of something similar implemented for the tracts-view)
  • C - when tvb-brco.xml has references from a TVB region --> to a brco term --> and back to other TVB regions, like in the following example:

    <TVBTerm id="http://thevirtualbrain.org#TCc" label="Central temporal cortex or subregion thereof">
        <OntClass label="Regional part of temporal lobe" uri="http://nerged.cellandgrossanatomy.owl#birnlex_1625">
            <OntClass label="ventral temporal cortex or subregion thereof" uri="http://thevirtualbrain.org#TCv"/>
            <OntClass label="superior temporal cortex or subregion thereof" uri="http://thevirtualbrain.org#TCs"/>
            <OntClass label="Pole of temporal cortex or subregion thereof" uri="http://thevirtualbrain.org#TCpol"/>
    We could display those as direct connections (somehow similar with the image C_... attached):
    

    Not possible with the current tvb-brco.xml, but perhaps we can get more data:

  • D - have another attribute on OntClass, "position" with X, Y, Z for some of the ontology terms.
    Do you have something else in mind ?

• Include Annotations in a simulation:
  I think this is the larger topic, of great interest for this collaboration, but I am not the best one to comment on it. Does somebody else want to comment ?
  Currently, as you probably know already, we do not have such support implemented in TVB.

Michaela wrote back :

when you write 3D view on the left side, do you mean the squares or "real" 3D brain images? (Like the brain images that pop out when looking at the results of a simulation, with brain regions highlighted in changing colouring?)
Such "real" 3D would be much more impressive to show than the squares. Is there any means to visualize 3D on the left side instead of the squares? I think that would be option B mentioned by you. I have the feeling that option D is difficult because we don't have any positions inside the BRCO that we might use for that. Or do you have anything in mind already how to do this?

Then I proposed what is currently on this task

For alternative D: I do not have something in mind. If such data can not be obtained in/from BRCO, then we should abandon this.

When I wrote "3D view on the left side" I meant the cubes which are drawn each for a the Connectivity Region centre in 3D.
I think you mean the Cortical Surface Viewer (we often call that the 3D Brain viewer).
Combining few existing pages of TVB (see attached images with prefix TVB_), I manually glued a BRCO_proposed image. on which we could adapt my previous proposals A and B.
Is this closer to what you have in mind ?