Morphological features of cellular and subcellular structures for cell phenotype profiling. (A) Example of the cell segmentation process and extraction of single cells. HeLa cells were segmented using contrast-enhanced images of microtubules and DAPI-stained nuclei. Each cell was assigned an identifier, and two representative cells (#38 and #81) are shown. Scale bar, 50 µm. (B and C) Examples of abstraction-based analysis of Golgi structure. Golgi morphology was characterized from GM130 images by analyzing fluorescence peaks (B) and by extracting skeletonized line objects (C). The boxed regions in the nucleus–Golgi distance measurements correspond to the cropped areas shown in Fig. 1 C. Scale bar, 50 µm. (D) Timeline for the analysis of mitotic spindle defects in metaphase-arrested HeLa cells. HeLa cells were synchronized with a double thymidine block, followed by ProTAME treatment to accumulate cells in metaphase. To induce specific spindle assembly defects, cells were treated with DMSO (control), taxol, or monastrol for 6 h, when most cells were expected to be in G2 phase. (E) Representative cell images. The left panel displays a full image of DMSO-treated cells, while the right panel shows magnified views of typical mitotic cells. Scale bars: 50 µm (full image) and 20 µm (magnified image). (F) Correlation matrix of all features used for cell phenotype profiling, as shown in Fig. 1 E. See Table S1 for descriptions of individual features.