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https://github.com/morphonets/SNT
The ImageJ framework for quantification of neuronal anatomy
https://github.com/morphonets/SNT
imagej imagej2 janelia neuroanatomy-toolbox neurons neuroscience scijava
Last synced: 2 months ago
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The ImageJ framework for quantification of neuronal anatomy
- Host: GitHub
- URL: https://github.com/morphonets/SNT
- Owner: morphonets
- License: gpl-3.0
- Fork: true (fiji/SNT)
- Created: 2019-11-15T02:57:26.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2024-11-12T12:08:05.000Z (3 months ago)
- Last Synced: 2024-11-12T13:19:34.836Z (3 months ago)
- Topics: imagej, imagej2, janelia, neuroanatomy-toolbox, neurons, neuroscience, scijava
- Language: Java
- Homepage: https://imagej.net/plugins/snt
- Size: 43.2 MB
- Stars: 42
- Watchers: 6
- Forks: 18
- Open Issues: 15
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
- Citation: CITATION.cff
Awesome Lists containing this project
- awesome-biological-image-analysis - SNT - ImageJ framework for semi-automated tracing and analysis of neurons. (Neuroscience)
README
The ImageJ framework for quantification of neuronal anatomy
SNT is [ImageJ](https://imagej.net/)'s framework for semi-automated tracing, visualization, quantitative analyses and modeling of neuronal morphology. For tracing, SNT supports modern multidimensional microscopy data, and highly-customizable routines. For data analysis, SNT features advanced visualization tools, access to all major morphology databases, and support for whole-brain circuitry data.
SNT can be used as a regular application or as a scripting library. Python (through [pyimagej](https://github.com/imagej/pyimagej)) and all of SciJava's scripting languages are supported. It is distributed with [Fiji](https://imagej.net/Fiji) and supersedes the original [Simple Neurite Tracer](#backwards-compatibility) plug-in. It also incorporates several other neuroanatomy-related Fiji plugins. **See [SNT's publication](https://doi.org/10.1038/s41592-021-01105-7) and [techical notes](./NOTES.md) for details**.
## Overview
[](https://www.nature.com/articles/s41592-021-01105-7)
## Features
For an overview of SNT capabilities have a look at the [showcase gallery](https://imagej.net/plugins/snt/#overview).
Detailed List
### Tracing
* Semi-automated Tracing:
* Support for up to 5D multidimensional images, including multichannel, and timelapse sequences
* Support for both ImageJ1 and [ImgLib2](https://imagej.net/libs/imglib2/) data structures
* Several bidirectional search algorithms (A\*, NBA\*, Fast marching) with adjustable cost functions allow for efficient computation of curvatures for a wide range of imagery, that are up to 20x faster relatively to the original _Simple Neurite Tracer_ plugin
* Tracing in "secondary layers". This allows for paths to be computed on "enhanced" (pre-processed) images while interacting with the unfiltered, original image (or vice-versa). Toggling between the two data sources is immediate
* Precise placement of nodes is aided by a local search that automatically snaps the cursor to neurites wihin a 3D neighborhood
* Auto-tracing:
* Generation of traces from thresholded/filtered images
* Machine learning: Built-in routines for training random forest classifiers on previously traced paths ([LabKit](https://github.com/juglab/labkit-ui)/[Trainable Weka segmentation](https://github.com/fiji/Trainable_Segmentation) bridges)
* Tracing can be interleaved with image processing routines
* Tracing is scriptable. Interactive scripts allow for real-time inspection of results
* Paths can be tagged, searched, grouped and filtered by morphometric properties (length, radius, etc.)
* Paths can be edited, i.e., a path can be linked or merged together, or split into two. Nodes can be moved, deleted, or inserted
* Post-hoc refinement of node positioning and radii by 'fitting' traces to the fluorescent signal associated with a path
### Analysis
* Extensive repertoire of metrics, namely those provided by [L-measure](http://cng.gmu.edu:8080/Lm/help/index.htm) and [NeuroM](https://github.com/BlueBrain/NeuroM). Metrics can be collected from groups of cells, single cells, or parts thereof
* Analysis based on neuropil annotations for whole-brain data such as [MouseLight](https://ml-neuronbrowser.janelia.org/)
* Direct access to public databases, including [FlyCircuit](http://www.flycircuit.tw), [Insect Brain Database](https://insectbraindb.org/app/), [MouseLight](https://ml-neuronbrowser.janelia.org/), [NeuroMorpho](http://neuromorpho.org/), and [Virtual Fly Brain](https://v2.virtualflybrain.org/)
* Built-in commands for immediate retrieval of statistical reports, including summary statistics, tests (two-sample _t_-test/one-way ANOVA), comparison plots and histograms
* Convex hull analyses
* Graph theory-based analyses
* Persistent homology-based analyses
* [Sholl](./NOTES.md) and Horton-Strahler analyses
* Image processing workflows: Reconstructions can be converted to masks and ROIs. Voxel intensities can be profiled around (or across) traced paths
### Visualization
* Quantitative visualizations: Display neurons color coded by morphometric traits, or neuropil annotations.
* Publication-quality visualizations: Neuronal reconstructions, diagrams, plots and histograms can be exported as vector graphics
* [Reconstruction Viewer](https://imagej.net/SNT:_Reconstruction_Viewer): Standalone hardware-accelerated 3D visualization tool for both meshes and reconstructions.
* Interactive and programmatic scenes (controlled rotations, panning, zoom, scaling, animation, "dark/light mode", etc.)
* Customizable views: Interactive management of scene elements, controls for transparency, color interpolation, lightning, path smoothing, etc. Ability to render both local and remote files on the same scene
* Built-in support for several template brains: Drosophila, [zebrafish](https://fishatlas.neuro.mpg.de/), and Allen CCF (Allen Mouse Brain Atlas)
* [sciview](https://github.com/scenerygraphics/sciview) integration
* Graph Viewer: A dedicated viewer for graph-theory-based diagrams
* Display reconstructions as dendrograms
* Quantitative connectivity graphs for single cells and groups of cells
### Scripting
* Almost every aspect of the program can be scripted in any of the IJ2 supported languages, or from Python through [pyimagej](https://github.com/imagej/pyimagej)
* Detailed [documentation](https://imagej.net/SNT:_Scripting) and examples, including Python [notebooks](https://github.com/morphonets/SNT/tree/master/notebooks), and [end-to-end examples](https://github.com/morphonets/SNTmanuscript)
* Headless scripts supported
* (Experimental) Script Recorder
### Modeling
* Biophysical modeling of neuronal growth is performed through [Cortex3D (Cx3D)](https://github.com/morphonets/cx3d) and [sciview](https://docs.scenery.graphics/sciview/ "SciView"), in which a modified version of [Cx3D](https://github.com/morphonets/cx3d) grows neuronal processes with [sciview](https://docs.scenery.graphics/sciview/)’s data structures.
### Compatibility
* Support for multiple file formats including SWC, TRACES, JSON (MouseLight specification), and NDF (NeuronJ data file)
* Backwards compatibility: Special effort was put into backwards compatibility with [Simple Neurite Tracer](https://github.com/fiji/SNT) (including [TrakEM2](https://github.com/trakem2/TrakEM2) and [ITK](https://imagej.net/SNT:_Tubular_Geodesics) interaction)
* Aggregation of [legacy plugins](./NOTES.md)
## Installation
SNT is a [Fiji](https://imagej.net/Fiji) plugin, currently distributed through the *Neuroanatomy* [update site](https://imagej.net/Update_Sites).
The first time you start SNT from Fiji's menu structure *(Plugins>Neuroanatomy>SNT...*) you should be prompted for automatic subscription and download of required dependencies. If not:
1. Run the Fiji Updater (*Help › Update...*, the penultimate entry in the *Help ›* menu)
2. Click *Manage update sites*
3. Select the *Neuroanatomy* checkbox
4. Optionally, select the *sciview* checkbox. This is only required for extra [sciview](https://docs.scenery.graphics/sciview/) functionality
5. Click *Apply changes* and Restart Fiji. SNT commands are registered under _Plugins>Neuroanatomy>_ in the main menu and SNT scripts under _Templates>Neuroanatomy>_ in Fiji's Script Editor.
Problems? Have a look at the full [documentation](https://imagej.net/SNT).
## Developing
### On the cloud
Use this button to open the project on the cloud using [Gitpod](https://gitpod.io). No local installation necessary (although project may take a while to load).
[](https://gitpod.io/#https://github.com/morphonets/SNT)
### Locally
1. Clone the main branch of this repository (use the green _code_ button above the list of files)
2. Import the project into an IDE such as [Eclipse](https://www.eclipse.org/downloads/packages/)/[IntelliJ](https://www.jetbrains.com/idea/download/)/[NetBeans](https://netbeans.apache.org/download/index.html):
- In Eclipse: Run _Import> Existing Maven Projects_ and specify the path to the downloaded `SNT` folder in _Root Directory_
- In IntelliJ: In the _Welcome Prompt_, choose _Open or Import_ and specify the path to the downloaded `SNT` folder
- In NetBeans: Run _File> Open Project..._, select the downloaded `SNT` directory, and click on _Open Project_
3. Wait for all the dependencies to be downloaded, and locate the [StartImageJAndSNTDemo](./src/test/java/sc/fiji/snt/demo/StartImageJAndSNTDemo.java) class in the tests folder.
4. Java 21 is recommended to run SNT, so you should specify it as the project JDK. However using Java17+ or newer requires the following VM arguments to be specified: `--add-opens java.base/java.lang=ALL-UNNAMED`. To do so:
- In Eclipse: Run -> Run Configurations..., Arguments tab
- In IntelliJ: Run -> Edit Configurations..., Add VM Options (Alt+V)
5. Run `SciviewSNTDemo.main()`
### Useful Resources to Start Hacking SNT
From a Java IDE:
- [Test demos](./src/test/java/sc/fiji/snt/demo/)
- _main()_ methods found on most classes: Frequently, these showcase the class's functionality
- [JUnit tests](./src/test/java/sc/fiji/snt/)
From Fiji's Script Editor:
- Scripts in the _Templates>Neuroanatomy>_ menu. These are part of the source code and can also be accessed from [Script templates](./src/main/resources/script_templates/Neuroanatomy/)
From python:
- [Jupyter notebooks](./notebooks)
Snippets and code templates:
- [Jupyter notebooks](./notebooks)
- [Script templates](./src/main/resources/script_templates/Neuroanatomy/)
- [Examples from the SNT manuscript](https://github.com/morphonets/SNTmanuscript)
- [Examples from I2K tutorials](https://github.com/morphonets/i2k2020)
- [Snippets across the forum](https://forum.image.sc/tag/snt)
## Contributing
Want to contribute? Please, please do! We welcome [issues](https://github.com/morphonets/SNT/issues) and [pull requests](https://github.com/morphonets/SNT/pulls) any time. You can also report bugs and propose improvements using the [forum](https://forum.image.sc/tag/snt). Please tag your post using `snt` so that it does not go unnoticed.
## Thanks To All Contributors
Thanks a lot for spending your time helping SNT!
