download mesh for entire hemibrain

[Joel Butterwick]

Hello,

I have downloaded mesh.obj for some of the brain regions I am interested in, but does anyone know if it is possible to download a mesh for the entire hemibrain?

Thanks,

Joel

[Greg Jefferis]

Dear Joel,

This may do the trick 

https://drive.google.com/file/d/1GIcSeUw5xGht6YeLdeFMitC9g5yvMtT_/view?usp=sharing

but I think the FlyEM team will have other options.

https://flyconnectome.github.io/hemibrainr/reference/index.html#section-synapses-and-meshes

https://flyconnectome.github.io/hemibrainr/reference/hemibrain.surf.html

constructed by Philipp Schlegel in our group and written out from R like so

Rvcg::vcgObjWrite(as.mesh3d(hemibrainr::hemibrain.surf), filename = 'hemibrain.obj', writeNormals = F)

NB this is calibrated in raw 8nm hemibrain voxels (like the skeletons you can retrieve from neuprint).

All the best,

Greg.

[Joel Butterwick]

Thanks Greg - your hemibrain.obj is exactly what I was looking for.

Best wishes,

Joel

[Stuart Berg]

Hi Joel, Greg,

(Thanks for chiming in, Greg!)

It looks like Greg's mesh corresponds to the union of all hemibrain neuropil ROIs, excluding the space between compartments.  You may also be interested in the "all_brain" ROI, which outlines the entire hemibrain sample, excluding non-tissue (i.e. excluding empty space, fixative, etc.).

In the following tarball, you'll find .obj files for all hemibrain ROIs, including "all_brain" and "all_neuropils" (which is similar to Greg's mesh above), as well as each of the individual neuropil compartments:

https://storage.googleapis.com/hemibrain/v1.1/hemibrain-v1.1-roi-meshes.tar.gz

(Those files use voxel units, i.e. 8nm, just like Greg's mesh above.)

To see what the all_brain ROI looks like in neuroglancer 2D, have a look at this link:

https://neuroglancer-demo.appspot.com/#!gs://flyem-views/hemibrain/v1.1/base.json

Best,

Stuart

[Greg Jefferis]

Thanks, Stuart!

Just to clarify for myself as much as anything

hemibrain.obj (from hemibrainr package) closed surface enclosing all neuropil / internal tracts. Spaces between neuropil regions are not modelled – there is no internal structure inside the mesh. Relatively low resolution.

all_brain (fly em) open surface defining the brain including the cell body layer etc

all_neuropils (fly em) open surface consisting of the union of all the separate neuropil domains – space between neuropil regions is modelled.

@Stuart, I wonder if if would be worth closing all_brain? The optic lobe portion is open on the fly's right hand side.

All the best,

Greg.

[Farzaan Salman]

Hello, 

Do you know if it is possible to add this mesh as a layer in neuroglancer? 

On Friday, October 2, 2020 at 6:41:01 PM UTC-4 jeff...@gmail.com wrote: