Reliable estimation of membrane curvature for cryo-electron tomography
Fig 2
Surface generation from membrane and compartment segmentations.
(A) A filtered tomographic slice showing the cortical endoplasmic reticulum (cER) and plasma membrane (PM) of a yeast cell (scale bar: 100 nm). Panels (B-C) show the same slice as in (A) with (B) the membrane segmentation of the cER and (C) the compartment segmentation of the cER; the insets show 3D renderings of the full segmentations (including all tomographic slices). Panels (D-F) show a surface generated from the cER membrane segmentation shown in (B): (D) The unmasked artefactual surface is shown in transparent white. The masked but uncleaned surface is shown in yellow with normals (every 100th) as red arrows. Some of the normals erroneously point outside the cER lumen (see right inset). (E) A different view of the uncleaned surface shown in (D), magnified. The red line marks an artifact. (F) The same magnified view as in (E) showing the cleaned surface in blue with a hole resulting from removing the artifact shown in (E). Panels (G-L) show surfaces generated using the compartment segmentation shown in (C), (G-I) without and (J-L) with Gaussian smoothing; the views are the same as in panels (D-F) column-wise: (G, J) Using the compartment segmentation, all normals point inside the cER lumen (see the insets). (H) Without smoothing, triangles sticking out (red circle) in the uncleaned surface lead to a hole in the cleaned surface shown in (I). (K-L) The cleaned smoothed surface is free from artifacts. The tomogram and segmentation are deposited in EM Data Bank (EMD-10767). See also the video in S1 Video.