Fig. 2

2D cell contour extraction with the Fiji SurfCut macro. a–c Illustration of the procedure used in order to determine the appropriate parameters for the cell contour extraction using the SurfCut “Calibrate” mode. a The macro first proposes to choose the radius to be used for the Gaussian Blur filter as well as the threshold for the signal binary conversion. This step is equivalent to the edge detect process of MGX. b The output of a can be visualized in the 3D viewer of Fiji to inspect it. c The desired depth of cropping can then be chosen. The voxel properties are automatically retrieved from the metadata but can be further adjusted. d Grayscale Z-projections (maximal intensity) of the original confocal stack (same as Fig. 1f). e Z-projection (maximal intensity) of the stack cropped with SurfCut. Scale bar is 50 μm