Fig. 2
From: From genotype to phenotype: decoding mutations in blasts by holo-tomographic flow cytometry
CSSI segmentation of a concave nucleus in the 3D RI tomogram of an OCI-AML-3 cell recorded by HTFC (Supplementary Movie S1 and Supplementary Movie S2). a QPM belonging to the overall stack of the flowing/rolling cell used to reconstruct its 3D RI tomogram. b Central slice of the 3D RI tomogram. c Nucleus initial guess (blue) obtained by segmenting the lowest values in (b) by an RI thresholding, with the reference cube highlighted in violet. d Intermediate nucleus set (blue). e Filtered intermediate nucleus set (blue) obtained by removing the outlier sub-cubes (red) from the intermediate nucleus set in (d). f Down-sampled intermediate nucleus set (blue), with highlighted in green the connection sphere used for the local linking of sub-cubes. g 3D nucleus polygonal (blue). h Final nucleus segmentation (blue), in which the concavity is indicated by the arrow. In (c-h), the cell shell is represented in gray. i–k 2D reprojections of the 3D binary nucleus segmented in (h) at three different orientations, normalized to their maxima. The gray line is the contour of the cell shell. Scale bar is 5 µm
