Organize TSNE data into grid
There seem to be a few options, but I found rasterfairy which is very easy to install and use. Has the added bonus of being able to fit to a rectangular grid, but also circular and other arbitrary shapes.

A very nice IronPython notebook example: https://github.com/Quasimondo/RasterFairy/blob/master/examples/Raster%20Fairy%20Demo%201.ipynb

And some example results: