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Extending SNT

Implementation and Algorithms

A high-level description of SNT’s algorithms is available on GitHub.

Using SNT in other projects

Currently, the easiest way to improve the code base is by following the guidance of the source-code repository. You will likely need an IDE and some basic familiarity with maven.

To use SNT as a software library in your own project, simply add SNT as a maven dependency in your project’s pom, e.g.:

<!-- https://mvnrepository.com/artifact/org.morphonets/SNT -->
<dependency>
    <groupId>org.morphonets</groupId>
    <artifactId>SNT</artifactId>
    <version>4.2.0</version> <!-- only required if pom-scijava is not being used as parent pom -->
</dependency>

See e.g., this forum thread for a concrete example of SNT being used as a software library.

Tubular Geodesics

The Tubular Geodesics plugins were developed several years ago for Simple Neurite Tracer but remain functional in modern SNT. They can be installed manually as an SNT add-on. Once installed, they allow you to trace on a filtered-version of your image in which neuronal processes (or other tubular structures) are significantly enhanced using ITK segmentation. More details on the following pages:

Tubular geodesics reference: doi:10.1109/cvpr.2012.6247722

TRACES File Format

The .traces files saved by SNT are gzip-compressed XML. SNT will also load and save uncompressed XML files, but the compressed form is the default.

The XML DTD is included in the DOCTYPE of each file. The root element is always <tracings>, which can contain the following elements: imagesize, samplespacing, path, and fill.

imagesize

There must be exactly one <imagesize> element, with attributes describing the image dimensions in voxels:

<imagesize width="520" height="434" depth="117"/>
Attribute Description
width Number of voxels along the X axis
height Number of voxels along the Y axis
depth Number of voxels along the Z axis

samplespacing

There must be exactly one <samplespacing> element, with attributes describing the voxel spacing in world coordinates:

<samplespacing x="0.28838738962693633" y="0.28838738962693633" z="1.2" units="micrometers"/>
Attribute Description
x Voxel spacing along X in world-coordinate units
y Voxel spacing along Y in world-coordinate units
z Voxel spacing along Z in world-coordinate units
units The unit of measurement (e.g., "micrometers")

path

Each <path> element represents a traced path and can have the following attributes:

Attribute Description
id A non-negative integer ID, unique among all paths in the file
name A string giving the name of this path
reallength The path length computed by summing Euclidean distances between consecutive points, in the units specified by samplespacing
swctype Integer flag defining the path type per the SWC specification. Defaults to 0 if absent
startson ID of the path that the beginning of this path branches off from. When present, either the deprecated startsindex or the recommended startsx/startsy/startsz must also be specified
startsx, startsy, startsz World coordinates of the branch point on the path given by startson. If any one is specified, all three must be
endson ID of the path that this path ends on. When present, either the deprecated endsindex or the recommended endsx/endsy/endsz must also be specified
endsx, endsy, endsz World coordinates of the point on the path given by endson where this path terminates. If any one is specified, all three must be
fitted ID of another path that is a fitted version of this one (with adjusted center-line and radii). Mutually exclusive with fittedversionof
fittedversionof ID of the unfitted source path that this path was derived from. Mutually exclusive with fitted
usefitted Required when fitted or fittedversionof is present. Value is "true" or "false". For an unfitted path with a fitted version, "true" means the fitted version should be displayed instead. For fitted paths, this should always be "false". NB: This attribute has confusing semantics and will be replaced in a future version.
startsindex Deprecated. 0-based index of the branch point in the path given by startson
endsindex Deprecated. 0-based index of the join point in the path given by endson

point

Each <path> may contain zero or more <point> elements representing the coordinates along the path:

Attribute Description
xd, yd, zd Position of the point in world coordinates. These are the values used for length calculations
r Radius of the neuron at this point (optional)
tx, ty, tz Tangent vector along the neuron at this point (optional)
x, y, z Deprecated. Position in image coordinates (0-based voxel indices)

fill

Each <fill> element represents a fill around a path. It contains all points found during the search starting from path nodes; the actual fill consists of those points whose distance is below the specified threshold. (The full set is stored so that the search can be resumed if the fill is reloaded.)

Attribute Description
id A non-negative integer ID, unique among all fills in the file
frompaths Comma-separated (optionally space-separated) IDs of the paths from which this fill started. For example, frompaths="2, 0" means nodes on paths 2 and 0 have distance 0 in this fill
metric The cost function used during the fill. (The attribute name is a legacy misnomer, kept for backward compatibility.)
threshold The distance threshold. Points with a distance below this value are considered part of the fill

node

Each <fill> may contain <node> elements representing individual search nodes:

Attribute Description
id A non-negative integer ID, unique within the enclosing fill
x, y, z Position in image coordinates (0-based voxel indices)
previousid ID of the previous node on the shortest route from the original paths to this point. Absent for points on the original paths (which have distance = 0)
distance Minimum distance found for any route from the original paths to this node. The complete route can be reconstructed by following previousid links
status Either "open" or "closed", with their conventional meanings in A* search

Curation File Format

Preset files (.curation file extension) used by Curation Assistant use a simple key=value format. Each check parameter has a value key and an .enabled key. Example:

# Calibrated from NeuroMorpho.org pyramidal cells ids XX-XX (20 cells, P5/P95)
branchAngle.min=15.2
branchAngle.max=95.5
branchAngle.enabled=true
directionContinuity.minAlignment=12.3
directionContinuity.enabled=true
radiusContinuity.maxRatio=1.8
radiusContinuity.enabled=true
terminalBranchLength.minLength=3.5
terminalBranchLength.enabled=true
somaDistance.maxDist=200.0
somaDistance.enabled=true
tortuosityConsistency.maxDiff=0.2
tortuosityConsistency.enabled=true
constantRadii.enabled=true
pathOverlap.proximity=4.0
pathOverlap.enabled=true
radiusJumps.maxRatio=2.5
radiusJumps.enabled=true
radiusMonotonicity.minRun=8
radiusMonotonicity.enabled=true