New methods for computational decomposition of whole-mount in situ images enable effective curation of a large, highly redundant collection of Xenopus images
Fig 1
Overview of image analysis pipeline.
(Upper panel) schematic representations of the stages of image analysis. Text boxes contain brief descriptions, see text for more detail, roman numerals correspond to steps in the workflow. Arrows show where data is extracted from the image for analysis. (A) Orthogonal projection of whitened 18 dimensional data extracted from the image. Colouring is made on result of clustering, with crosses and ellipses represent centres and covariances of the identified clusters. (B) Example representation of pixel colour density in the 3D colour space, showing identification of vectors corresponding to in situ stain, pigmented and un-pigmented embryo, used to identify regions of the embryo expressing the gene in question. (C) Example histogram of stain distribution. Data modelled as mixture of two Gaussians. The threshold is the smallest of mu + 2*sigma of the two components; it is represented as a solid green line. Dashed red lines represent range of values [.25, .67] the threshold is allowed to take.