Analysis Tools Plugin Help

• 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 each object.
• 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 deformation grid.
• 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 these regions.
• 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.