NITRC Waxholm Space Atlas of the Sprague Dawley Rat Brain Forum: user-forum

RE: Using the atlas in BrainJ (Fiji)

Gergely Csucs — Wed, 05 Feb 2025 14:25:22 GMT

Hi, we call our variant the "QUINT" workflow, https://quint-workflow.readthedocs.io/en/latest/
At a minimal level it consists of the 2D->3D registration (QuickNII/DeepSlice), cell analysis (Ilastik), and then combining the two (Nutil). This results in 3D point clouds, so coordinate listings. We have a viewer for it of course, but it can be used anywhere else - the format is JSON, so it's text.
We offer this workflow as part of EBRAINS ( https://www.ebrains.eu/tools/quint-workflow ), and provide user support for it too ( https://www.ebrains.eu/contact ).
I hope this helps, best regards,
Gergely

Using the atlas in BrainJ (Fiji)

Karolina Krizaic — Wed, 05 Feb 2025 12:23:42 GMT

Hello,
I’m working with 2D brain slice images and would like to visualize specific cells within a 3D rat brain model using Brainrender. I have downloaded the .nii files of the WHS Rat Brain Atlas and was wondering if they can be used in BrainJ for cell analysis.
Alternatively, is there a recommended software workflow to register 2D brain slices to a 3D atlas, then analyze the cells with Ilastik, and finally render them in Brainrender?
My goal is to accurately map extracted cell coordinates from 2D slices onto the 3D rat brain model. Any guidance on the best approach or tools for this process would be greatly appreciated.
Thank you!

RE: Upload whs-sd-atlas to zenodo in a different format ?

Nicolas Chiaruttini — Thu, 07 Nov 2024 12:19:49 GMT

Oups, I forgot to put the link. Here it is:
https://zenodo.org/records/8092060

RE: Requests for new anatomical regions

Michal Turovets — Thu, 14 Mar 2024 13:15:36 GMT

Hello, I just read your paper on the Waxholm Space atlas of the rat brain, and it mentions that the new segmentation present in the v4 atlas will not include subdivisions for the hypothalamus and amygdala. I am currently segmenting several structures in the rat hypothalamus, in particular the paraventricular nucleus of the hypothalamus (PVN), the supraoptic nucleus (SON), and the Ventromedial nucleus of the hypothalamus (VMH) from whole brain slices, and it would be very useful for registration :) Thank you so much for taking on the task of delineating a rat atlas. It has been invaluable to our research.

RE: 3D coordinates for VR model

Luis Schettino — Fri, 05 Jan 2024 23:07:00 GMT

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

RE: 3D coordinates for VR model

darwinjob — Fri, 05 Jan 2024 14:55:50 GMT

Originally posted by Luis Schettino:
<blockquote>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?</blockquote>
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

RE: Brain atlas with just the outline

Gergely Csucs — Fri, 13 Oct 2023 10:31:22 GMT

Hello,
It usually gives better results having the alignment done first, and then running edge-extraction on the colorful atlas slice at the end. The rationale behind this is if the outlines are already present at the beginning, as part of the atlas itself, when adjusting the atlas slice to fit the actual image, the pixels of the outline will be stretched-distorted too. While creating the outline as last step allows having a fixed, uniform thickness for the outline.
Image registration itself depends a lot on the image, for example if it's an actual 3D volume (MRI, PET, and the like), a series of images that can be reconstructed to a 3D volume (e.g. block-face methods), or 2D section images which need individual adjustments (e.g. histology without block-face support).
Best regards,
Gergely

Brain atlas with just the outline

Api Ala — Thu, 12 Oct 2023 12:47:26 GMT

Hello, Thanks for this Atlas. I was wondering, if there is a file where the atlas just shows segmentation as outlines? I want a similar result as in this picture (attached).
 
Cheers,
Abi

RE: 3D coordinates for VR model

Luis Schettino — Wed, 03 May 2023 18:17:30 GMT

[i]Originally posted by Gergely Csucs:[/i][quote]
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[/quote]
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?

RE: 3D coordinates for VR model

Gergely Csucs — Wed, 03 May 2023 12:03:11 GMT

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