Segmentation of HeLa cells

HeLa cells were embedded in Durcupan and observed with a Serial Block Face Scanning Electron Microscope (SBF SEM) following the National Centre for Microscopy and Imaging Research (NCMIR) protocol. The images were acquired with an SBF SEM 3View2XP microscope (Gatan, Pleasanton, CA, USA) attached to a Sigma VP SEM (Zeiss, Cambridge, UK). Voxel dimensions were 10x10x50 nm with intensity [0-255]. Five hundred and seventeen images of 8,192x8,192 pixels were acquired, from which an ROI was cropped by estimating manually the centroid of the cell to centre a box of 2,000x2,000x300 voxels. GT for the 2,000x2,000x300 ROI was manually delineated slice per-slice in Matlab. Disjoint nuclear regions were assessed by scrolling up and down to decide to include as part of the nucleus.