Update outdated snt pages

Author: tferr

_pages/plugins/snt/faq.md

@@ -75,20 +75,32 @@ Use the *Edit this page* option on the <a href="#top">top</a> of the documentati
 ## Tracing
 
 ### Can I trace in 3D?
-Yes. You can trace using the the XY,ZY,XZ [views](/plugins/snt/walkthroughs#accurate-point-placement) or more interactively: using the [3D Viewer](/plugins/snt/manual#legacy-3d-viewer) (legacy), or [sciview](/plugins/snt/manual#sciview) (experimental). There is also growing support for [Big Volume Viewer](/plugins/snt/manual#big-volume-viewer).
+Yes. You can trace using the the XY,ZY,XZ [views](/plugins/snt/walkthroughs#accurate-point-placement) or more interactively: using the [3D Viewer](/plugins/snt/manual#legacy-3d-viewer) (legacy). There is also growing support for [sciview](/plugins/snt/manual#sciview) and [Big Volume Viewer](/plugins/snt/manual#big-volume-viewer).
+
+### Can I undo tracing mistakes?
+Yes. With version 5 and later, temporary segments can be reverted before finishing a path simply by pressing {% include key key='Z' %}. In Edit Mode, editing operations can also be reverted using the same shortcut. By default, the last 20 operations can be undone.
 
 ### 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).
+Yes. Uncheck the *Confirm temporary segments* in the *Options* tab (*Temporary Paths* section): When this option is disabled. Segments are confirmed automatically. Note that double-click finishes a path directly, and the last confirmed segment can always be undone with the {% include key key='Z' %} key.
+
+### I miss NeuronJ's simplicity. Can I make SNT behave like NeuronJ?
+Yes! [NeuronJ](./plugins/neuronj) implemented several popular features: 1) Rapid iteration over image files stored in a common directory; 2) "Rubber band" tracing where temporary segments "stick" to the current cursor position, so that segments update continuously in real-time; and 3) Cursor snapping to neurite signal. All of these can be set in SNT:
+- Tracing of multiple images: Use {% include key key='ctlcmd|Shift|O' %} ([Save Tracings &amp; Open Next Image](./manual#save-tracings--open-next-image)) and {% include key key='ctlcmd|Alt|O' %} ([Save Tracings &amp; Open Previous Image](./manual#save-tracings--open-previous-image))
+- "Rubber band" tracing: Enable _Live Preview_ in [Algorithm Settings](./manual#algorithm-settings)
+- Cursor snapping: Enable [Cursor Auto-snapping](./manual#cursor-auto-snapping)
 
 ### 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.
 Alternatively, you can also obtain [Path profiles](/plugins/snt/manual#path-profiler), 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](https://forum.image.sc/t/how-to-set-the-correct-scale-micrometer-um-of-traced-cell-in-sholl-analysis/84764/4)
+There are multiple ways to handle this case. First, take note of the voxel size using {% include bc path='Image|Properties...' color='white'%}, then do one of the following:
+1. Use {% include bc path='Scripts|Tracing|Transform Paths' color='white'%} to scale paths in place
+2. Export tracings as SWC and re-import the file: The [Import prompt](./manual#load-tracings-) has an option for scaling paths
+3. Read the voxel dimensions from the image by, e.g., following [these instructions](https://forum.image.sc/t/how-to-set-the-correct-scale-micrometer-um-of-traced-cell-in-sholl-analysis/84764/4)
 
 ### Is there a way to process one image after another in a fast way?
-Yes. Have a look at these [instructions](https://forum.image.sc/t/simple-neurite-tracer-for-multiple-2d-images/22564/6?u=tferr).
+Yes. Use {% include key key='ctlcmd|Shift|O' %} / {% include key key='ctlcmd|Alt|O' %} (see [Save Tracings &amp; Open Next Image](./manual#save-tracings--open-next-image))
 
 ### 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 {% include bc path='File| Import|Image Sequence' color='white'%} 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 {% include bc path='Image|Properties...' color='white'%}. To save yourself from having to go through these steps again, you should save the imported stack as a single TIFF file using {% include bc path='File|Save As|Tiff...' color='white'%}
@@ -100,16 +112,10 @@ See [Sholl Analysis › FAQ](./sholl#faq).
 ## Spine Analysis
 
 ### Does SNT support spine analysis?
-Currently only [Spine densities](./walkthroughs#spinevaricosity-analysis) are supported. In-depth quantification of spine morphology can be done using [Spot Spine](/plugins/spot-spine), after tracing dendrites in SNT.
+See [Spine/Varicosity Analysis](./walkthroughs#spinevaricosity-analysis). In-depth quantification of spine morphology can be done using [Spot Spine](/plugins/spot-spine), after tracing dendrites in SNT.
 
 
 ## Soma Analysis
 
 ### Can SNT reconstruct somata?
-Currently SNT favors the [single-point soma representation](https://neuromorpho.org/SomaFormat.html). 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](../labkit) and [TWS](../tws)           | Bundled with Fiji                                                                                       | [SNT › Machine Learning](./machine-learning), [Forum](https://forum.image.sc/tag/labkit)    |
-| [Cellpose](https://www.cellpose.org/)           | Via [PTBIOP](https://wiki-biop.epfl.ch/en/ipa/fiji/update-site) update site                             | [Documentation](https://github.com/BIOP/ijl-utilities-wrappers?tab=readme-ov-file#cellpose), [Forum](https://forum.image.sc/tag/cellpose)|
-| [StarDist](https://github.com/stardist/stardist)| Via [PTBIOP](https://wiki-biop.epfl.ch/en/ipa/fiji/update-site)/[CSBDeep](/plugins/csbdeep) update sites| [Documentation](https://github.com/BIOP/ijl-utilities-wrappers?tab=readme-ov-file#stardist), [Forum](https://forum.image.sc/tag/stardist)|
+Yes, see [Autotracing › Soma/Root Detection](./auto-tracing#somaroot-detection). Note, however, that most SNT tutorials favor the [single-point soma representation](https://neuromorpho.org/SomaFormat.html).

_pages/plugins/snt/key-shortcuts.md

@@ -12,7 +12,7 @@ update-site: Neuroanatomy
 ---
 
 {% capture version%}
-**This page was last revised for [version 5.0.0](https://github.com/morphonets/SNT/releases)**.
+**This page was last revised for [version 5.0.5](https://github.com/morphonets/SNT/releases)**.
 {% endcapture %}
 {% include notice content=version %}
 
@@ -63,16 +63,19 @@ The [Command Palette](manual#command-palette) ({% include key keys='ctlcmd|Shift
 
 These shortcuts are available when running SNT in *Tracing Mode*:
 
-| {% include key keys='Ctrl|S' %} / {% include key keys='Command|S' %}           | <u>S</u>ave tracings |
-| {% include key key='Ctrl|Shift|S' %} / {% include key keys='Command|Shift|S' %} | <u>S</u>ave <u>S</u>napshot Backup |
 | {% include key key='L' %}                     | Toggles Tracing/Filling on Secondary <u>L</u>ayer (filtered image) |
 | {% include key key='V' %}                     | Finds the brightest <u>V</u>oxel above and below the current x,y position and automatically clicks on it. If multiple maxima exist, their average positioning is used. Note that this feature assumes that neurites are brighter than the background |
 | {% include key key='S' %}                     | Toggles cursor <u>S</u>napping: If enabled, the plugin will automatically move the cursor to the brightest voxel within the specified x,y,z snapping window<sup>1</sup>. When set correctly, this facilitates accurate [positioning of path points](/plugins/snt/walkthroughs#accurate-point-placement) |
+| {% include key key='Z' %}                     | Undo last segment (temporary paths) |
+| {% include key keys='Ctrl|Mouse Wheel' %}     | Change diameter of path being traced |
 | {% include key keys='Alt|Shift|Left Click' %} | Selects a point along the active path to be used as forking point (See [step-by-step instructions](/plugins/snt/walkthroughs#branching-start-a-path-on-an-existing-path) for more details on joining and branching). This shortcut can be [simplified](/plugins/snt/manual#temporary-paths) |
 | {% include key keys='Shift|B' %}              | <u>B</u>ookmarks cursor location |
 | {% include key keys='Shift|E' %}              | Activates *Edit Mode* (<u>E</u>diting of selected Path) |
 | {% include key keys='Shift|P' %}              | <u>P</u>auses tracing operations |
-
+| {% include key keys='Ctrl|S' %} / {% include key keys='Command|S' %}           | <u>S</u>ave tracings |
+| {% include key key='Ctrl|Shift|S' %} / {% include key keys='Command|Shift|S' %} | Backup tracings |
+| {% include key key='Ctrl|Shift|O' %} / {% include key keys='Command|Shift|O' %} | Save tracings & Open Next Image |
+| {% include key key='Ctrl|Alt|O' %} / {% include key keys='Command|Alt|O' %} | Save tracings & Open Previous Image |
 
 ### Path Editing
 
@@ -86,6 +89,7 @@ These shortcuts become available in *Edit Mode*, activated through the contextua
 | {% include key key='M' %} | <u>M</u>oves active node to cursor position |
 | {% include key key='R' %} | Changes the <u>R</u>adius of active node |
 | {% include key key='X' %} | Splits tree at active node, re-rooting the selected structure at the active node |
+| {% include key key='Z' %} | Undo last operation |
 
 ### Reconstruction Viewer