Analysis Tools Plugin Help
This plugin provides a number of analysis tools,
tools for deformation and dealing with with joined volumes and
several other functions. Many of these tools are experimental
and yes, poorly documented, and so it is highly advised you save
your work before trying to run them.
Hot Key Summary
Go to next slice (up)
Go to previous slice (down)
- Analysis Tools
- Estimate Z Scale -
Estimates the zScale of your section based on an closed contour object
which contains multiple roughly spherical and/or randomly oriented
compartments. The basic premise of this function is that a spherical
compartment should span the same distance in Z that it does in X and Y.
In reality however, many compartments are truncated, and thus more
sophisticated algorithms are used here to analyze the surfaces.
Details of this algorithm have been submitted for publication at PLoS
computational biology as "Improved Isotropic Reconstruction for 3D
Surface Models of Cellular Compartments by Mathematical Analysis of
Spherical Organelles by Electron Tomography".
- Analysis of Concave Points -
Allows you to specify a range of objects and outputs an 'analysis
of concave points' on each closed contour in these objects. This
analysis includes a count of the total number of concave points,
the fraction of contour length which is convex, the area of the
convex hull, the contour's 'compactness' and so on. This information
can give insight into the relative 'complexity' of contours in
- Analyze Tubes -
Designed to be used in situations where open contours have been used
to describe tubes of variable thickness, such that the radius of each
point reflects the tube's radius at that point. After specifying a
range of objects (with open contours) it outputs a mean width,
max width, estimated total volume and so on, by analyzing the size of
points and distance between them.
- Analyze Branching -
Designed to be used in situations where open contours have been used to
describe tubes, and some of these tubes 'branch' off others. The output
shows the length of each tube, and their organization hierarchy (i.e
which contour branches off which other contour) based on the proximity
of the contours first point to other contours.
- Volume-Distance Analysis -
This very crude function allows you to estimate how much volume is
within a certain distance of an object, but not in another object.
An example: 'How much volume is within 100 nm of my Golgi AND inside
the cell membrane AND not inside the Nucleus'. Note that all analyzed
objects must be segmented with closed contours on every slice. To
estimate volume random points are generated within a boxed region and
tested wether or not they are inside and/or within a specified distance
of a closed contour, thus the more points generated, the more accurate
results are likely to be.
- Deformation Grid:
- Generate -
Designed to generate a 'deformation grid' - a uniform grid of
(non-uniform) displacement vectors - between the 'section boundaries'
of joined tomograms. To work, this requires an object called
'deformation_points' containing a series of two-point open contour
which span across each section boundary and map the displacement
of some recognizable structure. Once a deformation grid is generated
it can be used to 'Deform Objects'.
- Deform Objects -
Uses a deformation grid (see above) to deform all points over a
range of objects specified by the user.
- Analyze Deformation Points -
Analyzes the XY offset of points in the 'deformation grid' object.
- Display Options -
Presents a number of options to change the appearance of the
- Section Tools:
- Delimit Tomogram Boundaries -
Constructions contours around the boundaries of the material
over a range of Z values specified by the user.
Note that the 'background pixel' is considered any pixel
outside the section material, and these typically have a value of 174.
- Delimit Grey Values -
Allows the user to specify a range of pixel values, and either:
(a) generates scattered point on each of these values, or
(b) generates a series of new closed contours either around
- Delete Slice -
Deletes the a range of slices from the model by removing contours
from those slices and shifting down all points above.
If specified, it will shifting open contour or scattered points
up or down so they won't be lost.
This plugin was created by Andrew Noske (andrew.noske<at>gmail<dot>com).
If you encounter bugs please e-mail me before e-mailing the
IMOD group (to reduce traffic).