“Materials” tab, select “Add”. Repeat this for each membrane
compartment (endoplasmic reticulum, vesicles, mitochondria,
etc.).
4. To visualize each segmentation, open the “Project View” window. Generate a surface by right clicking the “labels” data,
selecting “Generate Surface”, and clicking “create”. Under
the “Properties” tab, adjust the smoothing and select “Apply”.
4 Notes
1. Using holey carbon grids serves two purposes: (a) imaging
through the holes (when possible) provides images free from
carbon background and (b) the holes allow more water from
Fig. 6 Segmentation and visualization of a whole tomogram. (a) 20-nm thick tomographic slice through
neuronal cytoplasm. Microtubules, a mitochondrion, and multiple membrane-bound organelles and vesicles
can be seen. Scale bar represents 100 nm. (b) 20-nm thick slice through AI segmented membranes. (c) 20-nm
thick slice through AI segmented microtubules. (d) Three-dimensional surface rendering of segmented
volumes using Amira
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Ryan K. Hylton et al.
compartment (endoplasmic reticulum, vesicles, mitochondria,
etc.).
4. To visualize each segmentation, open the “Project View” window. Generate a surface by right clicking the “labels” data,
selecting “Generate Surface”, and clicking “create”. Under
the “Properties” tab, adjust the smoothing and select “Apply”.
4 Notes
1. Using holey carbon grids serves two purposes: (a) imaging
through the holes (when possible) provides images free from
carbon background and (b) the holes allow more water from
Fig. 6 Segmentation and visualization of a whole tomogram. (a) 20-nm thick tomographic slice through
neuronal cytoplasm. Microtubules, a mitochondrion, and multiple membrane-bound organelles and vesicles
can be seen. Scale bar represents 100 nm. (b) 20-nm thick slice through AI segmented membranes. (c) 20-nm
thick slice through AI segmented microtubules. (d) Three-dimensional surface rendering of segmented
volumes using Amira
44
Ryan K. Hylton et al.