(g) To generate tube, open the “Objects” window and choose
meshing.
(h) Select tube and set “Diam” to a pixel value that corresponds to the filament diameter.
(i) Press “mesh one”, this will generate a tube that represents
the traced filament. If “Cap” is activated, this will generate
a capped tube.
5. Example 2: Segmenting of vesicles or other membranous
organelles.
(a) Segmentation of vesicles and other membranous compartments is performed using the special drawing tools
plugin (see Note 38).
(b) Generate a new object by selecting in the information
window edit > object > new.
(c) Set “Object type” to “Closed”.
(d) Open drawing tools toolbar by clicking Special > Drawing
tools from the menu bar in the information window.
(e) Use the “Sculpt” function and trace the membrane of the
organelle across z-slices in the “ZaP Window”. It is not
necessary to do this on all slices, every second or third
should be sufficient.
(f) To generate a mesh for the vesicle, open the “Objects”
window and choose meshing. If membrane tracing was
not performed on every slice, activate “Skip” option in the
meshing dialog window and then press “mesh one”.
6. Example 3: Segmenting of small globular features,
e.g. ribosomes.
(a) Generate a new object by clicking on edit > object > new
in the information window.
(b) Select “Object type” to “Scattered”.
(c) In the “ZaP Window” or “Slicer”, place a point in the
center of the feature of interest.
(d) Under “Points” in the “Object”’ window, set “Sphere
Size” to a value that corresponds to the size of the feature
of interest and set drawing style to “Fill”.
(e) To adjust the smoothness of the sphere, modify the
“Object Quality” and “Global Quality” values.
3.6 Analysis of
Segmentation Model
IMOD has a series of command line programs for the analyses of
segmented data. A complete list with precise description can be
found at: https://bio3d.colorado.edu/imod/doc/program_list
ing.html. Below is a list of programs we find particularly useful.
1. Use the program “imodinfo” to extract quantitative information about the segmented objects, e.g. filament length, surface
areas, and volume.
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Daniel Serwas and Karen M. Davies
meshing.
(h) Select tube and set “Diam” to a pixel value that corresponds to the filament diameter.
(i) Press “mesh one”, this will generate a tube that represents
the traced filament. If “Cap” is activated, this will generate
a capped tube.
5. Example 2: Segmenting of vesicles or other membranous
organelles.
(a) Segmentation of vesicles and other membranous compartments is performed using the special drawing tools
plugin (see Note 38).
(b) Generate a new object by selecting in the information
window edit > object > new.
(c) Set “Object type” to “Closed”.
(d) Open drawing tools toolbar by clicking Special > Drawing
tools from the menu bar in the information window.
(e) Use the “Sculpt” function and trace the membrane of the
organelle across z-slices in the “ZaP Window”. It is not
necessary to do this on all slices, every second or third
should be sufficient.
(f) To generate a mesh for the vesicle, open the “Objects”
window and choose meshing. If membrane tracing was
not performed on every slice, activate “Skip” option in the
meshing dialog window and then press “mesh one”.
6. Example 3: Segmenting of small globular features,
e.g. ribosomes.
(a) Generate a new object by clicking on edit > object > new
in the information window.
(b) Select “Object type” to “Scattered”.
(c) In the “ZaP Window” or “Slicer”, place a point in the
center of the feature of interest.
(d) Under “Points” in the “Object”’ window, set “Sphere
Size” to a value that corresponds to the size of the feature
of interest and set drawing style to “Fill”.
(e) To adjust the smoothness of the sphere, modify the
“Object Quality” and “Global Quality” values.
3.6 Analysis of
Segmentation Model
IMOD has a series of command line programs for the analyses of
segmented data. A complete list with precise description can be
found at: https://bio3d.colorado.edu/imod/doc/program_list
ing.html. Below is a list of programs we find particularly useful.
1. Use the program “imodinfo” to extract quantitative information about the segmented objects, e.g. filament length, surface
areas, and volume.
16
Daniel Serwas and Karen M. Davies