From 4f0f1c25179fd9ce2a16309a6d83f50643ac99b8 Mon Sep 17 00:00:00 2001 From: Tiago Ferreira Date: Tue, 12 Nov 2024 07:08:05 -0500 Subject: [PATCH] Update README.md --- README.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index df465609..a1e0a848 100644 --- a/README.md +++ b/README.md @@ -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/) @@ -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 @@ -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