Render volumetric heatmaps on top of brain structures

Hi! This is a duplicate of an issue that I posted yesterday on the official vedo repository (https://github.com/marcomusy/vedo/issues/209). I wasn’t sure anymore whether it fits best as separate brainrender or as a vedo issue (given that not all features of vedo are enabled in brainrender?). I think it is also similar to this issue: https://github.com/BrancoLab/brainrender/issues/105.

What I want is to display some kind of volumetric heatmap, which I constructed as numpy array in the dimensions of the reference brain (allen 25 um), on top of some brain structures.

actor = Volume(
        my_numpy_3d_volume,
        spacing=[25, 25, 25], 
        alpha=.5,
        alphaUnit=.5
    )
actor = actor.legosurface(vmin=np.nanmin(score_map)+0.25, cmap='inferno')

The my_numpy_3d_volume contains a bunch of scores (but mostly nans). I am able to utilise .legosurface to display the volume at the correct location, which is great. However, what I really want is some kind of “smooth point cloud” that is mostly transparent where the original volume contains nans. What happens when I use .legosurface is that I get a volume with pretty jagged edges which distracts from the actual information that I want to shine through (a smooth blob in the center). I can smooth the volume, but that also smoothes the values inside, which is not what I want. Do you have any tipps on how to do this kind of stuff?

[marcomusy]

@FedeClaudi correct!

One other trick to see the inside is to transform the volume into a mesh, eg.:

from vedo import *
vol = load(datadir+'embryo.tif')
msh = vol.tomesh().clean()
msh.cutWithPlane(origin=(14000,0,0), normal=(1,1,1)).cmap('gist_ncar')
show(vol, msh, N=2, axes=1)

Note that this is feasible if the volume is relatively small.

[FedeClaudi]

this is how I do it for gene expression data. I don’t know how it works with nans but yeah you can convert them to some numeric value before thresholding if that’s causing you problems.

I haven’t played around with it, but you might be able to change the appearance of the mesh you get from lego surface. In vedo when legosurface is created: https://github.com/marcomusy/vedo/blob/c8d5b3fcdeea49a89e74f3b4dd9dc86d7c08b42e/vedo/base.py#L1428

it sets lw to 0.1, which I think it’s why you see the voxels edges. You can try to do .lw(0) to see if that works.