Figure 6.

Methods for analysis of trypanosomatid morphology, facilitated by use of color deconvolution. (A) Overview of the image analysis used to identify cells from the phase contrast image. A rolling ball filter was used to remove the phase contrast halo and the resulting image was thresholded then smoothed to generate a cell mask. (B,C) Nuclei and kinetoplasts were identified by thresholding the nucleus and kinetoplast images from color deconvolution. (D) Analysis of cell morphology used the medial axis transform (MAT) of the cell mask, generated by multiplication of the Euclidian distance map and pruned skeleton of the cell mask. (E) The MAT is a line that follows the midline of the cell mask. Values along the MAT encode the half width of the cell at each point; the original mask shape can be reconstructed by placing a circle of the appropriate radius at every point along the MAT (left). Plotting the values of the MAT provides the cell profile shape (right). (F) The distance of the kinetoplast and nucleus from the two ends of the cell were measured along the MAT. The distance from the centroid of the nucleus/kinetoplast to the MAT gave the distance from the cell midline.

Wheeler et al. BMC Biology 2012 10:1   doi:10.1186/1741-7007-10-1
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