Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

hemibrain_reroot doesn't work with hemibrain.surf #4

Open
jefferis opened this issue Feb 10, 2020 · 3 comments
Open

hemibrain_reroot doesn't work with hemibrain.surf #4

jefferis opened this issue Feb 10, 2020 · 3 comments
Assignees

Comments

@jefferis
Copy link
Contributor

Unfortunately hemibrain_reroot doesn't work with the new hemibrain surface mesh. I'm not sure if it is expanded with respect to the underlying meshes. For FAFB I have used the signed distance to help with soma identification rather than assuming that they have to be outside the mesh. Not sure if that could help here.

bad.soma = c("5813015982","885788485","5813013913")
# Read in these neurons
neurons.bs = neuprintr::neuprint_read_neurons(bad.soma)
# Re-root
neurons = hemibrain_reroot(neurons.bs, meshes = hemibrain.surf)
@alexanderbates
Copy link
Collaborator

I can just deflate the mesh ... @schlegelp do you remember how much you inflated its constituent ROIs?

@schlegelp
Copy link

In theory I reversed all dilations I did. I'm guessing the increase in size is the result of the initial downsampling (voxelsize = 1 micron) and the final remeshing to reduce the complexity.

I'm afraid the increase in size is also not uniform - otherwise I would have tried to compensate straight away.

@jefferis
Copy link
Contributor Author

jefferis commented Apr 9, 2020

A note that this is now improved with the updated hemibrain.surf in 8ba96b7 but one of the three neurons above still fails (for reasons that aren't completely clear to me).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants