Hello,

I am exploring the possibility of creating a VR model of the rat brain (simplified) to teach neuroanatomy to undergraduate students. I would like to know what your recommendations would be in order to create point clouds for some of the major divisions of the brain, which we would subsequently optimize. I saw that Meshview is able to produce point clouds but there was a mention that it requires Flash to run. Is it still a good choice?
Any help would be appreciated.

Luis

Hi,

A technical detail is that version 4 of this atlas contains 41 232 144 segmented voxels, which in the extreme case could become a set of point clouds (of the 222 segmented structures) totaling in the same amount of points, so ~41 million. How and if it should be downsampled in a random or uniform matter, largely depends on what amount of points the targeted VR environment(s) can handle. Assuming that I understand the question correctly and the plan is to have point clouds for the structures themselves (I'm not very familiar with VR and when I saw VR, that was working with meshes).

For simplifying the atlas itself, it's probably advisable to do that when the atlas is still NIfTI, then ITK snap or external tools can help with merging structures into larger ones. Merging them when they are subsampled point clouds already may easily result in unwanted artifacts, such as visible boundaries between supposedly continuous regions. A quick search revealed these ideas for such relabeling task: https://discourse.itk.org/t/remove-multiple-labels-in-1-bone-and-have-only-1-label-per-bone/5186

A side note about MeshView: it doesn't need Flash for quite some time (6-7 years). https://meshview.apps.hbp.eu/?atlas=WHS_SD_Rat_v4_39um shows WHS SD Rat v4 - however as it's not a VR tool, chances are that it can't help with your use case.

Best regards,
Gergely

Hi Gergely,

Thank you very much for your reply. I took a look at the meshview explorer that you sent and I agree, that is definitely a large amount of information, much more that we would be able to handle (or require).
I will familiarize myself with the software you mention to see if we can have something practicable that way. 

Another quick question, if you have the time: is it possible to work with earlier versions of the atlas? are they smaller?

Very much appreciated,
Luis

Hi Luis, The actual segmented area is mostly stable, so even the first version of the atlas has this ~41 million-ish voxels, just they are divided into fewer regions. For example in the early versions there's a very large"Neocortex": https://meshview.apps.hbp.eu/?atlas=WHS_SD_Rat_v2_39um
Then v3 segmented a few (literally, 3 I think) regions from it, related to the auditory areas: https://meshview.apps.hbp.eu/?atlas=WHS_SD_Rat_v3_39um, then v4 got far more detailed, https://meshview.apps.hbp.eu/?atlas=WHS_SD_Rat_v3_39um
The actual downloadable label files show progress, and there's also a changelog in the "Documents" area: https://www.nitrc.org/docman/view.php/1081/191550/

Do you have a concrete VR system/framework in mind? Have you perhaps seen a video, and thought "this is what I want"? I'm still just shooting into the dark, so I can't really suggest what is viable and what is not.

Best regards,
Gergely

Originally posted by Gergely Csucs:
I have not seen any digital recreations of brains for VR, actually. I just think that being able to immerse my students in the space itself would be a good way to help them both recognize the relative locations of specific brain regions/nuclei and for them to practice anatomical terminology. 
I will try to describe what I am envisioning: I was thinking that I could use a large physical space to 'drop' the student in the middle of a large rat brain (say, 5 meters long). From there, the student could interact by turning on and off some of the structures, for example, the striatum or the colliculi and recognizing their relative distances. They could intuitively recognize that the amygdala is ventral and relatively lateral by seeing it with respect to say, the thalamus. They would be able to see how the third ventricle traverses the hypothalamus. That kind of thing. 
I believe that the earlier version for which you sent me a link (v.2) may be more amenable to my idea because the cortex is not too divided up. I don't think I want students to get too hung up on the breakdown of the neocortex at this time. 
So I was hoping to take the neocortex as a single element, the caudo-putamen as another (perhaps accumbens separately), the thalamus, the amygdala. These would be the major divisions. Does that make sense?

Originally posted by Luis Schettino:

I have not seen any digital recreations of brains for VR, actually. I just think that being able to immerse my students in the space itself would be a good way to help them both recognize the relative locations of specific brain regions/nuclei and for them to practice anatomical terminology.  I will try to describe what I am envisioning: I was thinking that I could use a large physical space to 'drop' the student in the middle of a large rat brain (say, 5 meters long). From there, the student could interact by turning on and off some of the structures, for example, the striatum or the colliculi and recognizing their relative distances. They could intuitively recognize that the amygdala is ventral and relatively lateral by seeing it with respect to say, the thalamus. They would be able to see how the third ventricle traverses the hypothalamus. That kind of thing.  I believe that the earlier version for which you sent me a link (v.2) may be more amenable to my idea because the cortex is not too divided up. I don't think I want students to get too hung up on the breakdown of the neocortex at this time.  So I was hoping to take the neocortex as a single element, the caudo-putamen as another (perhaps accumbens separately), the thalamus, the amygdala. These would be the major divisions. Does that make sense?

It very much does, Luis! Pity that Gergely "forgot" to tell you that already in March (your post is.. from May?) we had a runnable Rat Brain VR demo https://github.com/darwinjob/xrviewer

HTC Vive (other headsets too) can do what you describe - it is called room-scale VR. The demo was developed during a weekend by a sole developer. Let me know if you're still interested.

Best regards
Dmitri

Hi Dmitri,

Thank you for contacting me. I am currently away from my office, but I will give your VR demo a try next week. I like what I can see thus far!

Luis