That's at least close to true. It might be better to think of it as a smoothed "segmentation" of a 3D image, i.e. some algorithm decided what pixels are officially part of e.g. the mitochondria set, and outlined them. That could be based on level sets or seeded watershed or whatever else works well.
There are some alternate visualizations here http://www.allencell.org/3d-cell-viewer.html of data that came off of our microscopes that we also use to visualize our models in house but wasn't;t included in the video. It's hard to visualize varying density 3D data in 2D -- there's no one good way to do it, especially on the fly over the web -- but if you have any feedback about what would be more informative / easier to understand, let us know.
There are some alternate visualizations here http://www.allencell.org/3d-cell-viewer.html of data that came off of our microscopes that we also use to visualize our models in house but wasn't;t included in the video. It's hard to visualize varying density 3D data in 2D -- there's no one good way to do it, especially on the fly over the web -- but if you have any feedback about what would be more informative / easier to understand, let us know.