Fig 3. Rational selection of representative images to reduce redundancy.

Unsorted images from a large collection for a given gene/development stage are first classified into cleared (grey background) and un-cleared (orange/red background) images. Embryo boundaries were detected within the image and embryo pixel colours analysed to yield predicted in situ stain, pigmentation or unmarked embryo. Embryos with predicted outline touching the image border were excluded (unless the outline in all images in the group touched the border). Images were sorted within groups by stain content for selection, and cropped for display where needed. (A) Lateral view images, NF stage 20+. (B) Quasi-spherical development stages (up to NF stage 20): images are clustered according to expression pattern similarity under rotational and other transformations (see also Fig 4), and the most stained image is selected from each well-separated group.