General
How do I install SNT?
See Installation details.
How do I cite SNT?
The proper citation for SNT is:
Note that neither the main Fiji article, nor the first Simple Neurite Tracer publication are appropriate citations for SNT. To reference additional modules that enhance SNT:
- Sholl Analysis doi:10.1038/nmeth.3125
- Cx3D doi:10.3389/neuro.10.025.2009
- Tubular Geodesics doi:10.1109/cvpr.2012.6247722
What is the difference between SNT and Simple Neurite Tracer?
Simple Neurite Tracer was the first Fiji plugin dedicated to visualization and reconstruction of neurons, developed by Mark Longair and published in 2011, to become the single most cited open-source software for semi-automated 3D reconstructions. In the wake of ImageJ2 development, a new team of developers lead by Tiago Ferreira took on the effort of modernizing its code base. The project quickly snowballed beyond the re-write of the software, and focused on establishing a complete framework for reconstruction, visualization, quantification and modelling of neuronal morphology. Several name changes were proposed for this “next-gen” Simple Neurite Tracer (Not so Simple Neurite Tracer, Smart Neurite Tracer, Super Neurite Tracer to name a few), but in the end it was decided to adopt the acronym of the original software, as an homage to Mark’s outstanding work. You can follow the entire history of the plugin on GitHub: Simple Neurite Tracer’s historic and SNT’s current repositories.
How accurate is SNT?
When SNT is compiled, a suite of tests is run to detect deficiencies in the code base. Morphometry results are benchmarked against values obtained in L-Measure and NeuroM. However, no test suite is ever perfect. If you detect inaccuracies, please report them!
What is a SWC file?
It is the most widely adopted format for encoding neuronal reconstructions, in which information is stored in plain text. It was first described by (Cannon et al., 1998) and since then became a somewhat loose lingua franca of a neuron’s three-dimensional structure. The latest SWC specification provides more details about the format. SNT supports all known variants of the format including ESWC, SWC+, and latest specification (v1.0.3, as of this writing). The extension stems from the last names of Stockley, Wheal, and Cole, who developed a neat computer system for reconstructing neuronal cells ( Stockley et al., 1993). Confusingly, an unrelated Adobe SWC file format also used to exist.
In which format should I save my tracings: TRACES or SWC?
When tracing 4D or 5D images, TRACES is preferable because the channel and/or time frame associated with the data are stored. With simpler 2/3D images TRACES is also preferable to preserve Path Manager tags across restarts. Note that the Scripts › menu provides a batch converter for TRACES → SWC conversion. The following table summarizes the differences between the two formats:
| SWC | TRACES | |
|---|---|---|
| No. reconstructions per file | Formally only one. When multiple reconstructions exits, SNT splits them across multiple files appending unique suffixes to filenames | Multiple reconstructions per file allowed |
| Image metadata | Formally none. SNT stores the spatial calibration of the image in the header | Rich. Including channel and frame of the traced structure. |
| Path Manager tags | Not stored | Stored |
| Fits | Not stored, unless fitting replaces existing nodes | Stored |
| Fills | Not stored | Filling parameters stored |
| Format | Plain text | XML or compressed XML (as per preferences) |
| Presence | Ubiquitous among reconstruction software. The de facto standard in data sharing | Exclusive to SNT. But open and easily parsable |
Which file formats for neuronal reconstruction are supported by SNT?
SNT can read TRACES, SWC, NDF (NeuronJ data format), and JSON files (as used by the MouseLight project). Other file formats can be converted to SWC using xyz2swc.
My neuronal reconstructions are saved under a format that is not supported. How can I open them?
Unsupported and proprietary file formats can be converted to SWC using xyz2swc.
Which image file formats are supported by SNT?
Any file format supported by ImageJ/bioformats with up to 5 dimensions. RGB images are strongly discouraged and are converted to multichannel before loading.
How do I (batch) convert TRACES to SWC?
Use the Batch › Convert Traces to SWC script either from the Scripts menu in the main dialog, or the Templates › Neuroanatomy menu in the Script Editor.
How can I improve SNT documentation?
Use the Edit this page option on the top of the documentation page and edit its contents at will. Don’t be shy. All changes are undoable!
Tracing
Can I trace in 3D?
Yes, always. Either using the XY,ZY,XZ views or more interactively: using the 3D Viewer (legacy), or sciview (experimental).
Having to confirm individual segments is too cumbersome. Is it possible to trace without interruption, by clicking in succession?
Yes. Uncheck the Confirm temporary segments in the Options tab (Temporary Paths section).
How can I browse voxel intensities around processes?
Right-click on the image canvas and select Pause SNT from the contextual menu. Voxel intensities will be reported in the ImageJ status bar. Alternative, you can also obtain Path profiles, in which voxel intensities are plotted along selected path(s).
I traced an image in pixel coordinates but need to scale the reconstruction to physical units. How do I do it?
Have a look at these instructions
Is there a way to process one image after another in a fast way?
Yes. Have a look at these instructions.
How can I import an image sequence into SNT?
Loading of images that require input options is handled by ImageJ directly. To load a directory of images (e.g., one file per Z-slice), run File › Import › Image Sequence and select the first file in the sequence, adjusting any needed parameters in the subsequent dialog prompt. Once the sequence is imported adjust voxel dimensions using Image › Properties…. To save yourself from having to go through these steps again, you should save the imported stack as a single TIFF file using File › Save As › Tiff…
Spine Analysis
Does SNT support spine analysis?
Currently only Spine densities are supported. In-depth quantification of spine morphology can be done using Spot Spine, after tracing dendrites in SNT.
Soma Analysis
Can SNT reconstruct somata?
Currently SNT favors the single-point soma representation. The task of soma segmentation is better tackled using ImageJ built-in tools for analysis of contours, or by means of dedicated machine-learning tools, including:
| Tools | Fiji Integration | Resources |
|---|---|---|
| Labkit and TWS | Bundled with Fiji | SNT › Machine Learning, Forum |
| Cellpose | Via PTBIOP update site | Documentation, Forum |
| StarDist | Via PTBIOP/CSBDeep update sites | Documentation, Forum |
