SNT: fix outdated links /misc adjustments for v5

tferr · tferr · commit a3c63e9e615c · 2026-02-09T13:52:30.000-05:00
diff --git a/_pages/plugins/snt/auto-tracing.md b/_pages/plugins/snt/auto-tracing.md
@@ -77,7 +77,7 @@ Higher connectivity produces smoother paths through the image but may trace thro
 
 ### About the Algorithm
 
-SNT's grayscale autotracing as been implemented with substantial re-engineering/improvements:
+SNT's grayscale autotracing has been implemented with substantial re-engineering/improvements:
 
 - **Full-resolution tracing** Works directly on original image data without mandatory downsampling, preserving fine details
 
diff --git a/_pages/plugins/snt/big-data.md b/_pages/plugins/snt/big-data.md
@@ -26,4 +26,5 @@ SNTv5 implemented _preliminary_ support for big data. The support remains basic
 | 3D Visualization         | Supported via [sciview](./manual#sciview) and [BigVolumeViewer](./manual#big-volume-viewer) | Visualization of 3D reconstructions, including [color mappings](./manual#color-mapping-), etc.                                       |
 
 <sup>1</sup>For interactive tracing, please use [HortaCloud](https://hortacloud.org/): This is SNT's development team recommended tool for tracing Terabyte-size datasets
+
 <sup>2</sup>See [PySNT](https://pysnt.readthedocs.io/en/latest/)
diff --git a/_pages/plugins/snt/index.md b/_pages/plugins/snt/index.md
@@ -28,9 +28,10 @@ The [source repository](https://github.com/morphonets/SNT) contains more details
 
 {% include gallery align="fill" content=
 "
+/media/plugins/snt/snt-auto-tracing-overview.png | [Fully automated tracing](/plugins/snt/auto-tracing) from raw grayscale imagery (no thresholding required) as well as segmented images
+/media/plugins/snt/snt-bvv.png | [Big-data (out-of-core) support](/plugins/snt/big-data): Automatic switch to disk-backed processing for TB-scale datasets that don’t fit in RAM (experimental)
 /media/plugins/snt/snt-4D-examples.png | [Semi-automated tracing](/plugins/snt/walkthroughs#semi-automated-tracing): Support for multi-channel and [timelapse](/plugins/snt/walkthroughs#time-lapse-analysis) images
-/media/plugins/snt/snt-auto-tracing-overview.png | [Fully automated tracing](/plugins/snt/walkthroughs#full-automated-tracing) of segmented images
-/media/plugins/snt/snt-v3-overview.png | [Scripted routines](/plugins/snt/scripting#bundled-templates) co-exist with graphical user interface operations
+/media/plugins/snt/snt-v3-overview.png | [Scripted routines](/plugins/snt/scripting#snt-scripts) co-exist with graphical user interface operations
 /media/plugins/snt/snt-script-example.png | [Scripting](/plugins/snt/scripting) in any of Fiji's supported languages facilitated by SNT's [Script Recorder](/plugins/snt/scripting#script-recorder)
 /media/plugins/snt/snt-notebook.png | Scripting in native Python using [PySNT](https://pysnt.readthedocs.io/en/latest/)
 /media/plugins/snt/snt-delaunay-triangulation.png | Delaunay tessellation: Tracings can be used in [image processing routines](/plugins/snt/manual#process-)
diff --git a/_pages/plugins/snt/manual.md b/_pages/plugins/snt/manual.md
@@ -63,10 +63,6 @@ Specifies the image to trace on without having to restart SNT. Commands include:
 
 In either scenario. You should toggle the *validate spatial calibration* checkbox to ensure the image to be imported is compatible with the existing one.
 
-#### Autotrace Segmented Image File...
-
-If you have a binary mask of the image you want to trace saved to disk (i.e., a pre-processed version of the image in which background pixels have been zeroed), you can use this command to attempt automatic reconstruction. This is similar to {% include bc path='Utilities | Autotrace Segmented Image... ' %} but uses file paths as input. See [Full-automated tracing walkthrough](/plugins/snt/walkthroughs#full-automated-tracing) for details.
-
 #### Load Tracings ›
 
 Imports of neuronal reconstructions from multiple sources, including:
@@ -112,7 +108,28 @@ Convenience shortcuts to open common directories (scripts, backups, folder of im
 
 #### Reset SNT and Restart...
 
-Resets all preferences and restarts SNT using default options. It is recommended to reset SNTs after a major version release.
+Resets all preferences and restarts SNT using default options. It is recommended to reset SNT after a major version release.
+
+### Auto-trace ›
+
+#### Grayscale Image (GWDT)...
+Runs fully automated tracing directly from a **grayscale (intensity) image** already open in SNT (no binarization required). The approach uses **Gray-Weighted Distance Transform (GWDT)** with Fast Marching and expects bright-on-dark imagery. See [Autotracing › Grayscale Images](/plugins/snt/auto-tracing#grayscale-images) for details.
+
+#### Grayscale Image (GWDT) File...
+
+Same as {% include bc path='Grayscale Image (GWDT)...' %}, but loads the grayscale image from a **file path** (including [big-data/out-of-core](/plugins/snt/big-data) datasets). See [Auto-tracing › Grayscale Images](/plugins/snt/auto-tracing#grayscale-images) for details.
+
+#### Detect Soma...
+Standalone tool for automatic soma/root detection in neuronal images. Detects the thickest and brightest structures using an EDT×intensity score, and can export results as a path node or ROI (point, countour, circle) for annotation or seeding autotracing. See [Auto-tracing › Soma Detection](/plugins/snt/auto-tracing#soma-detection) for details.
+
+#### Autotrace Segmented Image...
+
+Runs fully automated tracing on a segmented image that is already open. A segmented image can be a binary mask or a thresholded image, where background pixels have been set to zero. See [Auto-tracing › Segmented Images](/plugins/snt/auto-tracing#segmented-images) for details.
+
+#### Autotrace Segmented Image File...
+
+Same as {% include bc path='Autotrace Segmented Image...' %}, but loads the segmented image from a file path instead of using an image already open. See [Fully automated tracing](/plugins/snt/auto-tracing#segmented-images) for details.
+
 
 ### Analysis ›
 
@@ -122,6 +139,9 @@ See [Analysis › Atlas-based Analysis](/plugins/snt/analysis#atlas-based-analys
 #### Path-based ›
 See [Analysis › Path-based Analysis](/plugins/snt/analysis#path-based-analysis).
 
+#### Compare Reconstructions/Cell Groups...
+Allows morphometric comparisons of two single reconstruction files or multiple groups of reconstruction files (including statistical reports and two-sample t-test/one-way ANOVA analysis). Color-coded montages of analyzed groups can also be generated. See [Comparing Reconstructions](/plugins/snt/analysis#comparing-reconstructions) for details.
+
 #### Convex Hull
 See [Analysis › Convex hull Analysis](/plugins/snt/analysis#convex-hull-analysis).
 
@@ -139,37 +159,12 @@ See [Analysis › Sholl Analysis](/plugins/snt/analysis#sholl-analysis).
 
 See [Analysis › Strahler Analysis](/plugins/snt/analysis#strahler-analysis).
 
-#### Measure...
-
-Provides a comprehensive selection of measurements to apply to one connected component (i.e., rooted tree structure) from the Path Manager. See [Analysis › Measurements](/plugins/snt/analysis#measurements) for details.
-
-#### Quick Measurements
-
-Shortcut for running {% include bc path='Measure...' %} with common metrics.
-
-### Utilities
-
-#### Command Palette
-
-{% include img src="/media/plugins/snt/command-palette.png" align="right" width="450px" %}
-The Command Palette is the fastest way to access actions and discover their respective shortcuts:
-
-1. Press {% include key keys='ctlcmd|Shift|P' %} in either SNT or [Reconstruction Viewer](/plugins/snt/reconstruction-viewer)
-2. Start typing to filter actions, scripts and available commands
-3. Press {% include key keys='up' %} or {% include key keys='down' %} (or use the  {% include key keys='mouse wheel' %}) to select a command
-4. Press {% include key keys='Enter' %} to run it. If the record button is toggled, executed commands are recorded by the [Script Recorder](/plugins/snt/scripting#script-recorder).
-
-By default, commands and actions are filtered using approximate string matching. Exact matching can be enabled by toggling the _Match Case/Whitespace_ buttons. Press the &nbsp;<i style="color:gray;" class="fas fa-map-pin"></i>&nbsp; button to display the Command Palette above all windows. Press the &nbsp;<i style="color:gray;" class="fas fa-lock"></i>&nbsp; button to keep the Palette open after running a command.
-
-
-#### Compare Reconstructions/Cell Groups...
-Allows morphometric comparisons of two single reconstruction files or multiple groups of reconstruction files (including statistical reports and two-sample t-test/one-way ANOVA analysis). Color-coded montages of analyzed groups can also be generated. See [Comparing Reconstructions](/plugins/snt/analysis#comparing-reconstructions) for details.
 
+#### Utilities
 
 #### Create Dendrogram
 Generates a Dendrogram plot of a connected component (i.e, one rooted tree structure in the Path Manager). See [Analysis › Graph-based Analysis](/plugins/snt/analysis#graph-based-analysis) for details.
 
-
 #### Create Figure...
 
 <img align="right" src="/media/plugins/snt/snt-create-figure.png" title="Create Figure... prompt" width="350px" alt="Create Figure... prompt" />
@@ -188,7 +183,6 @@ Creates multi-panel figures from chosen reconstructions, according to the follow
   <img src="/media/plugins/snt/snt-create-figure-demo.gif" title="Create figure: 3D (interactive) multi-panel montage" width="60%" alt="Create figure: 3D (interactive) multi-panel montage" />
 </div>
 
-
 <span id="plotter"></span>
 
 #### Reconstruction Plotter
@@ -201,10 +195,14 @@ _Reconstruction Plotter_ is a whole-purpose 2D viewer for neuronal reconstructio
 - Color legends when color mappings are present
 - Can be combined in multi-panel viewers (mainly via scripting)
 
+#### Measure...
 
-#### Autotrace Segmented Image...
+Provides a comprehensive selection of measurements to apply to one connected component (i.e., rooted tree structure) from the Path Manager. See [Analysis › Measurements](/plugins/snt/analysis#measurements) for details.
+
+#### Quick Measurements
+
+Shortcut for running {% include bc path='Measure...' %} with common metrics.
 
-Similar to {% include bc path='File|Autotrace Segmented Image File...| ' %} but using image(s) already open  as input. See [Full-automated tracing walkthrough](/plugins/snt/walkthroughs#full-automated-tracing) for details.
 
 ### Scripts›
 
@@ -224,6 +222,20 @@ Contains commands for organizing tracing views on screen, plus commands for disp
 
 - **{% include bc path='Toggle Fiji Console' %}** Toggles the visibility of Fiji's Console. The console displays errors and exceptions as well as informational messages when _Debug mode_ is activated.
 
+### Help›
+
+##### Command Palette
+
+{% include img src="/media/plugins/snt/command-palette.png" align="right" width="450px" %}
+The Command Palette is the fastest way to access actions and discover their respective shortcuts:
+
+1. Press {% include key keys='ctlcmd|Shift|P' %} in either SNT or [Reconstruction Viewer](/plugins/snt/reconstruction-viewer)
+2. Start typing to filter actions, scripts and available commands
+3. Press {% include key keys='up' %} or {% include key keys='down' %} (or use the  {% include key keys='mouse wheel' %}) to select a command
+4. Press {% include key keys='Enter' %} to run it. If the record button is toggled, executed commands are recorded by the [Script Recorder](/plugins/snt/scripting#script-recorder).
+
+By default, commands and actions are filtered using approximate string matching. Exact matching can be enabled by toggling the _Match Case/Whitespace_ buttons. Press the &nbsp;<i style="color:gray;" class="fas fa-map-pin"></i>&nbsp; button to display the Command Palette above all windows. Press the &nbsp;<i style="color:gray;" class="fas fa-lock"></i>&nbsp; button to keep the Palette open after running a command.
+
 ## Main Tab
 
 This *home* tab aggregated widgets for tracing and frequent operations.
@@ -695,15 +707,15 @@ Combines (connects) two or more _disconnected_ paths into one (undoable operatio
 
 #### Concatenate...
 
-Concatenates two or more paths into a single un-branched segment. Concatenated paths must be oriented in the same direction. Can be used to merge non-contiguous fragments from [full-automated tracing](/plugins/snt/walkthroughs#full-automated-tracing) belonging to the same neurite.
+Concatenates two or more paths into a single un-branched segment. Concatenated paths must be oriented in the same direction. Can be used to merge non-contiguous fragments from [full-automated tracing](/plugins/snt/auto-tracing) belonging to the same neurite.
 
 #### Merge Primary Path(s) into Shared Root
 
 Takes two or more primary paths and merges them into a common root node placed at the centroid defined by starting nodes of the primary paths to be merged. This is useful, e.g., when all the paths around a soma have been traced without passing through it. Note that this will alter parent-child relationships between paths.
 
 #### Reverse...
 
-Reverses the orientation of primary path(s) so that the starting node becomes the end-node and vice versa. Can be used to correct 'anti-sense' paths created by [full-automated tracing](/plugins/snt/walkthroughs#full-automated-tracing).
+Reverses the orientation of primary path(s) so that the starting node becomes the end-node and vice versa. Can be used to correct 'anti-sense' paths created by [full-automated tracing](/plugins/snt/#auto-tracing).
 
 #### Specify Constant Radius...
 
diff --git a/_pages/plugins/snt/pysnt.md b/_pages/plugins/snt/pysnt.md
@@ -10,3 +10,9 @@ update-site: Neuroanatomy
 
 [PySNT](https://pysnt.readthedocs.io/en/latest/) is a Python wrapper for SNT that enables direct integration with the Python software ecosystem, including NumPy, SciPy, scikit-image, and more.
 For details, see the [PySNT documentation page](https://pysnt.readthedocs.io/en/latest/).
+
+<p align="center">
+    <a href="https://pysnt.readthedocs.io/en/latest/">
+        <img align="center" src="/media/plugins/snt/pysnt-screenshot.png" alt="pysnt.readthedocs.io" width="800px">
+    </a>
+</p>
diff --git a/_pages/plugins/snt/screencasts.md b/_pages/plugins/snt/screencasts.md
@@ -7,47 +7,47 @@ icon: /media/icons/snt.png
 forum-tag: snt
 ---
 
-This page contains a list of video tutorials and recorded workshopts that describe SNT capabilities.
+This page contains a list of video tutorials and recorded workshops that describe SNT capabilities.
 
 
-# Workshops
+> **Note:** These videos are a useful complement to the written documentation, but some recordings were made for older SNT releases and may not reflect recent features or UI changes. When in doubt, follow the [manual](./manual). Do [reach out](https://forum.image.sc/tag/snt) if something is unclear or doesn't match what you see in SNT.
+>
+> Screencasts are also a great way to share workflows and tips. Anyone is [welcome to make them](./contribute). Do [let us know](./contribute#reach-out) if you've made a tutorial video, or better: Add it directly to this list!
 
-## Exploring neuronal morphology with SNT and pyimagej
 
-{% include video platform='youtube' id='AwpQS59AjuU' %}
+# Video Tutorials by Users
 
+- **2024 (SNT v4.2)**:
+  - [Full-Automated Neurite Tracing (Segmented Images)](https://www.youtube.com/watch?v=vSUmtFFdoBY)
+  - [Semi-Automated Neurite Tracing](https://www.youtube.com/watch?v=XJo280aBsTw)
+  - [Neurite Tracing](https://www.youtube.com/watch?v=jkY-QRlxZN4)
 
-# Video Tutorials
+# Workshops by Dev Team
 
-## Introduction To Tracing
+- **2023 (SNT v4.2)**:
+  - **Janelia's HIT**: [How to... use SNT to segment neurons](https://www.youtube.com/watch?v=fMn14QHqCp4)
+  
+- **2022 (SNT v4.1)**:
+  - **I2K 2022**: [Exploring neuronal morphology with SNT and pyimagej](https://www.youtube.com/watch?v=AwpQS59AjuU)
+  - **I2K 2022**: [Neuroanatomy in the ImageJ Ecosystem](https://www.youtube.com/watch?v=UUFWZ-Z2s6w)
 
-{% include video platform='youtube' id='7wC0F4RcUKw' %}
 
-## Advanced Path Editing
+# Video Tutorials by Dev Team
 
-{% include video platform='youtube' id='Dh0XczTAGM0' %}
+- **2020 (SNT v3)**:
+  - **[Secondary Images](https://www.youtube.com/watch?v=tQH2YSf4pns)**
 
-## Secondary Images
+- **2019 (SNT v3)**:
+  - **[Introduction To Tracing](https://www.youtube.com/watch?v=7wC0F4RcUKw)**
+  - **[Advanced Path Editing](https://www.youtube.com/watch?v=Dh0XczTAGM0)**
+  - **[Analyzing Reconstructions](https://www.youtube.com/watch?v=inZl4zS7oc4)**
 
-{% include video platform='youtube' id='tQH2YSf4pns' %}
-
-## Analyzing Reconstructions
-
-{% include video platform='youtube' id='inZl4zS7oc4' %}
 
 
 # Outdated Screencasts
 
-These are old [Simple Neurite Tracer](/plugins/snt/faq#what-is-the-difference-between-snt-and-simple-neurite-tracer) screencasts that are likely too outdated to be useful. Listed here for historical record.
-
-## Basic Usage of [Simple Neurite Tracer](/plugins/snt/faq#what-is-the-difference-between-snt-and-simple-neurite-tracer)
-
-{% include video platform='youtube' id='y6ZPdDfUOjI' %}
-
-## Using MIP overlays in [Simple Neurite Tracer](/plugins/snt/faq#what-is-the-difference-between-snt-and-simple-neurite-tracer)
-
-{% include video platform='youtube' id='pXpMRb1AC4I' %}
-
-## Using The [Legacy 3D Viewer](/plugins/snt/walkthroughs#tracing-in-the-legacy-3d-viewer)
+These are much older [Simple Neurite Tracer](/plugins/snt/faq#what-is-the-difference-between-snt-and-simple-neurite-tracer) screencasts that are likely too outdated to be useful. Listed here for historical record.
 
-{% include video platform='youtube' id='SrPeSwu31Zs' %}
+  - 2016: [Basic Usage](https://www.youtube.com/watch?v=y6ZPdDfUOjI)
+  - 2011: [Using MIP overlays](https://www.youtube.com/watch?v=pXpMRb1AC4I)
+  - 2011: [Example of 3D Tracing](https://www.youtube.com/watch?v=SrPeSwu31Zs) (using the [Legacy 3D Viewer](/plugins/snt/walkthroughs#tracing-in-the-legacy-3d-viewer))
diff --git a/_pages/plugins/snt/strahler.md b/_pages/plugins/snt/strahler.md
@@ -25,7 +25,7 @@ There are several entry points to Strahler Analysis in SNT. You can find those i
 {% include notice icon="info" content=strahler %}
 
 {% capture strahler%}
-While _Strahler Analysis (Image)..._ remains a functional workflow, you may find its simplicity rather limiting. A more flexible approach may be to convert [skeletonized images into traced paths](/plugins/snt/walkthroughs#full-automated-tracing) and run [Strahler Analysis (Tracings)](/plugins/snt/analysis#strahler-analysis) on them.
+While _Strahler Analysis (Image)..._ remains a functional workflow, you may find its simplicity rather limiting. A more flexible approach may be to run [auto-tracing](/plugins/snt/auto-tracing) and run [Strahler Analysis (Tracings)](/plugins/snt/analysis#strahler-analysis) on them.
 {% endcapture %}
 {% include notice icon="warning" background-color="#fffbeb" content=strahler %}
 
diff --git a/media/plugins/snt/pysnt-screenshot.png b/media/plugins/snt/pysnt-screenshot.png
