3D view of cell AND nucleus

[tischi]

@constantinpape

I just got very excited because I found that the 3DViewer API allows having multiple objects with different transparency. So, if both nucleus and cell label masks are active we can probably, upon ctrl+shift+click show both the cell and the nucleus in one 3D viewer window, and even make the cell a bit more transparent such that one can see the nucleus inside. Isn't that amaaaaazing? :-)

Just a demo (not real data):

[constantinpape]

Yes, that would be amazing! We could also use this for other structures; e.g. cilia which I am segmenting right now.

[tischi]

I am working on making the whole 3D View aspect more professional and:

1. I feel it would be good to precompute the meshes (i.e. a list of some coordinates on the surface).
2. Maybe the simplest (to start with) would be if those meshes were a column in the table text file, maybe just a space separated list of voxel coordinates: 2 2 2 3 4 5 3 2 4 9 10 12 with x0 y0 z0 x1 y1 z1 x2 y2 z2 .... Probably there are more clever ways, e.g. storing only differences to a starting point (https://stackoverflow.com/questions/283299/best-compression-algorithm-for-a-sequence-of-integers)

What do you think?

[constantinpape]

1. I feel it would be good to precompute the meshes (i.e. a list of some coordinates on the surface).

Yes, that sounds like a good idea if you want to improve performance.

2\. Probably there are more clever ways, e.g. storing only differences to a starting point

For performance / efficient storage it might also help to serialize a (compressed) byte stream instead of the table version.

[tischi]

progress:

[tischi]

Testimonials :-) F**uck!!!!! XD OMFG! Amazing!!! WOWWW