Forrest Collman

I started this process! https://github.com/AllenInstitute/PyGraphTEASAR I have not finished fully testing it on real neurons, but if you wanted to contribute there that would be useful!

This repo has only numpy and scipy as dependancies.

yes I think that I would like to basically remove much of what is in trimesh_vtk and replace it with pyvista and/or vtk plotter style commands. Certainly maintaining multiple implementation...

no nothing fundamental.. just differences in the api and some worry about forcing people to upgrade is just as bad as not upgrading, so then wanting to make it work...

I must admit i scanned through and didn't see the change amongst all the formatting changes.. can you highlight the relevant meaningful change?

This seems related to differences in compilers that were used to create the numpy release you have installed on your environment. This is likely caused by using some combination of...

You could also try relaxing some of the constraints in the environment.yml file, depending on what the conda failure was. Usually this is some incompatibility of available pre-compiled binaries.

Do you have the ability to acquire training data yourself? meaning dye cells and take dual channel stacks so you can later only acquire single channel transmitted light stacks?

I would caution that images that are taken on a different microscope of different cells with potentially different z spacing, different xy resolution, different interslice timing are not likely to...

so I think i better understand your question now.. you would like a pointer to a dataset with sparser cells but nucleus and membrane labels so you can try to...