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. Author manuscript; available in PMC: 2022 Nov 2.
Published in final edited form as: Nat Cancer. 2021 Dec 24;3(1):122–133. doi: 10.1038/s43018-021-00301-w

Fig. 2. Single-cell segmentation of a 3D IMC generated breast carcinoma model.

Fig. 2

a, Segmentation and cell catalog generation pipeline. A voxel model is used as an input for a 3D watershed segmentation. Detected objects are assigned unique cell identifiers. Statistics for all channels and morphological descriptors are calculated for every segmented cell (N cells, M channels). b, Iridium signal from a single representative slice (no. 58 out of 152) from one out of the two breast carcinoma models used in this study, the same model is also displayed in Fig.1b (left). Segmentation mask overlay of the iridium channel (right). In the segmentation mask, different cells are labeled with random colors. c, Example of a full segmentation mask over the surface-rendered iridium channel in the same model (containing a total of 152 slices). Images were produced with napari v.0.4.1rc2 (ref. 40).