Comparing three-dimensional raw images to PointCloud representations. (a-c) Maximum projections of the three channels of a three-dimensional embryo image; (a) the nuclear stain (white); (b) a snail mRNA stain (red); and (c) an eve mRNA stain (green). Note the small bright speckles visible in all three channels at the same locations. These are outside the cytoplasm and are detected and removed by our image analysis algorithms. The small white rectangles show a region of interest that is displayed in (d-g). (d,e) The raw image of the nuclear stain (d) and the mRNA stains for eve and sna (e). (f,g) Two different renderings of the PointCloud derived from this image made using our visualization tool PointCloudXplore: (f) uses small spheres whose volumes are proportional to the measured volumes of the corresponding nuclei; (g) uses a Voronoi tessellation of the coordinates in the PointCloud. The arrows indicate the locations of the same three cells in each of the panels (d-g).