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tferr authored Nov 12, 2024
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Expand Up @@ -106,13 +106,13 @@ For an overview of SNT capabilities have a look at the [showcase gallery](https:

* 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
* Paths can be edited, i.e., linked, merged, or split. 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
* Extensive repertoire of [metrics](https://imagej.net/plugins/snt/metrics). 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/)

Expand All @@ -129,6 +129,8 @@ For an overview of SNT capabilities have a look at the [showcase gallery](https:
* [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

* Labkit and TWS integration ([Semantic Segmentation](https://imagej.net/plugins/snt/machine-learning))

### Visualization

Expand Down Expand Up @@ -207,11 +209,13 @@ Use this button to open the project on the cloud using [Gitpod](https://gitpod.i

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:
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()`
![image](https://github.com/user-attachments/assets/1679e954-dc89-4061-bfa2-b4a10da4f0da)

5. Run [StartImageJAndSNTDemo.main()](./src/test/java/sc/fiji/snt/demo/StartImageJAndSNTDemo.java)

### Useful Resources to Start Hacking SNT

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