Tom Goddard, Bernhard Knierim, Monica Lin, Manfred Auer
September 22, 2010
New segmentation, visualization and measurement methods were added to Chimera for analysis of bacteria in termite hindgut seen with focused ion beam scanning electron microscopy (FIBSEM). Shown here are some of the visualization and measurement capabilities.
Map name: LBL_09-2009
File name: sem1_flat.cmap
Grid size: 1808, 1483, 161
Voxel size: 5, 6.5, 15 nm
Number of segmented cells: 574
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| Plane 0. | Plane 80. | Plane 160. | All planes. |
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| Plane 0 colored. | Plane 80 colored. | Cell surfaces. | All planes colored. |
Central slices of 100 straightened cells.
Coloring by cell diameter. | 
Only longest cells shown. Colored by length, blue 6 um to red 12 um. |
Cell number: 58
Region id number: 25519
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| Position. Grid bounds: 232, 0, 56 to 1076, 900, 158 Truncated: yes | Shape. Enclosed volume: 0.428 um^3 Surface area: 8.53 um^2 | Contacts. Number of contacting cells: 29 | Principal axes bounding box. Size: 7.20, 2.03, 1.25 um |
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| Center line. Length: 9.00 um Ave curvature: 1.55 1/um Max curvature: 4.22 1/um Min curvature: 0.172 1/um | Cross-section. Diameter: 260 nm Diameter perp: 219 nm | Center slices. Curved ribbons 500 nm wide following center line. Two orthogonal 3-dimensional ribbons. Note indentations of envelope by contacting cells. Enveloped cell: yes |
Masked density. Maximum intensity projection.
Straightened cell. Orthogonal central slices.
TODO: Show extra-cellular vesicles. Show flagella.
TODO: Show gallery of different cell morphologies.
