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Fig. 1 | BMC Biology

Fig. 1

From: ImageJ SurfCut: a user-friendly pipeline for high-throughput extraction of cell contours from 3D image stacks

Fig. 1

2D cell contour extraction with MGX. a Original confocal stack opened in MGX: cotyledon pavement cells of A. thaliana, stained with propidium iodide. b Confocal stack from a after a Gaussian Blur (0.3-pixel radius). c Detected surface using the Edge Detect process. d Mesh created using a 5-μm Marching Cubes Surface process, then smoothing one time and subdivision one time. e Original confocal stack (green), surface’s mesh created in MGX (yellow), and the 2-μm-thick layer of signal cropped at a distance of 6 (top) to 8 (bottom) μm from the surface in MGX (red). The view of the sample is tilted to allow better visualization of the mesh, the original signal, and the cropped stack. f Grayscale Z-projections (maximal intensity, in Fiji) of the entire original confocal stack (from a). g Z-projections (maximal intensity, in Fiji) of the 2-μm-thick layer of signal extracted, in red in e. Scale bar in ad is 100 μm and in fg is 50 μm

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