Improve data loading speed/general performance

[andrewhill157]

The assignment 3 version needs to be optimized somewhat I think if we are going to be loading the gene expression data (and RNA-seq data in the future). This may be as easy as getting everything in one file to speed up loading, or it could involve some more complex solution (hopefully not).

[tdurham86]

I just added a feature to change the size of non-highlighted nuclei instead of the transparency. I like the effect, and I think it does a good job of allowing the user to see the highlighted cells with minimal occlusion while still providing information about the surrounding cellular context. However, this change introduced a fairly significant performance hit. Since x3dom does not allow you to dynamically rescale the spheres after they are plotted, every time the highlights change, the spheres that transition between the highlighted and non-highlighted states must be redrawn. As a quick solution to see what the scale change would look like, the current implementation simply redraws the entire scene whenever the highlights change. I think we can make this faster by only redrawing the parts of the scene that need to change, but that will require some more tinkering.

[tdurham86]

I've been working a lot on the data loading and optimization. It's not perfect, and it can probably still go faster, but we're at least in the ballpark for an acceptable user experience at this point. Just a quick update to indicate we're making progress.