Analysis - BlueBrain/NeuroMorphoVis GitHub Wiki
- Morphology Skeleton & Terminology
- Soma Kernels
- Branches Kernels
A neuronal morphology has two distinct structures: a cell body (or soma) and arbors (or neurites, trees). Traditionally, the soma is simply represented by a centroid, average radius and two-dimensional projective profile. The arbors emanate from a cell body (soma), where each arbor is composed of a set of raw samples. Two connected sampled define a segment, and a set of segments between two branching points defines a section. Multiple connected sections define an arbor.
A morphological sample is a point in the three-dimensional space that is digitally reconstructed by an operator from an optical micorscopy stack.
Note In similar contexts, the sample can be referred to as point.
A morphological segment is a connection between two samples only.
Note In similar contexts, the segment can be referred to as strand.
A morphological section is a list of connected segments between two branching points.
Note In similar contexts, the section can be referred to as branch.
A morphological arbor is a list of connected branches starting from the soma and terminating at one or multiple leaf sections. It has a similar structure to acyclic graphs or trees. Arbors are classified into apical dendrites (in green), basal dendrites (in red) and axons (in blue).
Note In similar contexts, the arbor can be referred to as neurite or tree.
The Cartesian center of the soma. This point is by default located at the origin, unless otherwise specified.
Note To avoid any mesh reconstruction artifacts, NeuroMorphoVis by default shifts any morphologies that are not centered at the origin back to the origin.
The radius of the soma as reported in the morphology file in μm.
The minimum radius of the soma as based on the reported profile points and the root samples of all the connected arbors (or stems).
The maximum radius of the soma as based on the reported profile points and the root samples of all the connected arbors (or stems).
The average radius of the soma as based on the reported profile points and the root samples of all the connected arbors (or stems).
The approximate surface area of the soma based on the reported radius in the morphology file in μm².
The approximate volume of the soma based on the reported radius in the morphology file in in μm³.
Number of profile points of the soma as reported in the morphology file.
THe branching kernels are applied recursively on the entire morphology skeleton, but some of thre results are reported for the morphology and per arbor.
We summarize the morphology bounding box by
- BBox PMin: The pMin of the bounding box.
- BBox PMin:The pMax of the bounding box.
- BBox Center:The center of the bounding box.
- BBox Bounds:The dimensions of the bounding box.
Note that the width, height, depth of the morphology bounds are computed along the X, Y and Z axes respectively.
This plot shows an orthographic projection of the front view (XY) of the neuron.
This plot shows an orthographic projection of the side view (ZY) of the neuron.
This plot shows an orthographic projection of the top view (XZ) of the neuron.
This plot shows the dendrogram of the neuron. The color codes reflect each arbor in the neuron as shown in the projections.
The total number of samples (or digitized points) in the morphology or per arbor.
The total number of segments (or strands) in the morphology or per arbor. The number of segment is simply less than the number of samples by one.
The total number of sections (or branches) in the morphology or per arbor. The following neuron has seven sections.
The total number of apical dendrites in the morphology. Normally, an excitatory neuronal morphology has a single apical dendrite, but we explicitly added this parameter in case the morphology has more than one. The following neuron has an apical dendrite colored in green. The other arbors are faded.
The total number of basal dendrites in the morphology. The following neuron has six basal dendrites colored in red. The other arbors are faded.
The total number of axons in the morphology. Normally, a neuronal morphology has a single axon, but we explicitly added this parameter in case the morphology has more than one or has no axon reconstructed. The following neuron has an axon colored in blue. The other arbors are faded.
The total number of the arbors (independent trees) in the morphology whether connected to the soma or not. This is the sum of the apical dendrites, basal dendrites and axons in the morphology. The following neuron has eight arbors.
The number of arbors (branches) that emanate directly from the soma. Each stem is basically an independent subtree of branches. For example, the morphology shown in the following image has seven stems.
The total number number of terminal tips (samples terminating leaf nodes in the graph) in the morphology or per arbor. The following neuron has 13 terminal tips.
The total number of bifurcations (or sections with two children) in the morphology or per arbor. The following neuron has only two bifurcations.
The total number of trifurcations (or sections with three children) in the morphology or per arbor. Trifurcations are not common, but they exist in some morphologies.
The maximum branching order of all the arbors in the morphology or per arbor.
The maximum distance along an arbor from its root sample to its most far leaf in the morphology.
The lowest number of samples a section has in the morphology or per arbor.
The largest number of samples a section has in the morphology or per arbor.
The average number of samples a section has in the morphology or per arbor.
The radius of the smallest sample in the morphology or per arbor.
The radius of the largest sample in the morphology or per arbor.
The avaerage radius of all the samples sample in the morphology or per arbor.
The Burke taper range per arbor.
The local bifurcation angle is computed from the first two samples along the section. We compute the minimum, maximum and average local bifurcation angles in the morphology or per arbor.
The global bifurcation angle is computed from the first and last samples of the section. We compute the minimum, maximum and average global bifurcation angles in the morphology or per arbor.
The aggregate length of all the sections in the morphology or per arbor in μm.
The length of the shortest section in the morphology or per arbor in μm.
The length of the longest section in the morphology or per arbor in μm.
The average section length in the morphology or per arbor in μm.
The length of the shortest segment in the morphology or per arbor in μm.
The length of the longest segment in the morphology or per arbor in μm.
The average segment length in the morphology or per arbor in μm.
The total surface area of the morphology or per arbor in μm².
The surface area of the smallest section in the morphology or per arbor in μm².
The surface area of the largest section in the morphology or per arbor in μm².
The average section surface area in the morphology or per arbor in μm².
The surface area of the smallest segment in the morphology or per arbor in μm².
The surface area of the largest segment in the morphology or per arbor in μm².
The average segment surface area in the morphology or per arbor in μm².
The total volume of the morphology or per arbor in μm³.
The volume of the smallest section in the morphology or per arbor in μm³.
The volume of the largest section in the morphology or per arbor in μm³.
The average section volume in the morphology or per arbor in μm³.
The volume of the smallest segment in the morphology or per arbor in μm³.
The volume of the largest segment in the morphology or per arbor in μm³.
The average segment volume in the morphology or per arbor in μm³.
The total number of zero-radii samples (epsilon value 1e-3 or 1 nm) in the morphology or per arbor.
The total number of zero-length segments (or duplicate samples) or per arbor.
The total number of short sections (length is smaller than the sum of the radii of the terminal samples). These short sections are causing artifacts in the mesh reconstruction process, so it is better to handle them before creating any meshes.
Note We are adding new analysis functions to provide further analysis results on a continuous basis. If you have any questions, please contact us.
Note The table of contents was generated automatically with markdown-toc.
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