Merge pull request #422 from imagej/autotracers

update pages on snt autotracers

Author: tferr

_pages/plugins/snt/auto-tracing.md

@@ -29,30 +29,33 @@ 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 both [grayscale images](./auto-tracing#grayscale-images) (no thresholding required) and [segmented images](./auto-tracing#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-autotracing-multiple-somata.webp | [Fully automated tracing](/plugins/snt/auto-tracing) of [multiple cells in the same image](./auto-tracing#multiple-cells)
+/media/plugins/snt/snt-autotracing-groundtruth-learning.png | [Auto-tuned tracing](./auto-tracing#learning-parameters-from-selected-paths): Learned tracing parameters from manually traced paths
+/media/plugins/snt/snt-soma-detection.png | Automated [soma detection](/plugins/snt/auto-tracing#soma-detection)
 /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-soma-detection.png | Automated [soma detection](/plugins/snt/auto-tracing#soma-detection) (no thresholding required)
-/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-spectral-unmixing.png | Support for [Brainbow-like images](./walkthroughs#tracing-in-multichannel-brainbow-images)
-/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-)
-/media/plugins/snt/snt-density-map.png | Density maps for group(s) of cells obtained from [built-in scripts](/plugins/snt/scripting#bundled-templates)
-/media/plugins/snt/snt-recviewer-convexhull-and-surface.png | [Convex hulls](/plugins/snt/analysis#convex-hull-analysis) and [surface annotations](/plugins/snt/reconstruction-viewer#geometric-annotations)
-/media/plugins/snt/snt-montage-light.png | Quantitative and publication quality visualizations
-/media/plugins/snt/snt-montage-dark.png | Data-rich 3D visualizations
-/media/plugins/snt/snt-rec-viewer-demo2-dark.gif | [Interactive 3D scenes](/plugins/snt/reconstruction-viewer)
+/media/plugins/snt/snt-bvv.png | [Big data support](/plugins/snt/big-data): TB-scale datasets that exceed available RAM (experimental)
+/media/plugins/snt/snt-curation-assistant.png | [Calibrated, real-time quality-control](./curation#curation-assistant) of traced morphologies
+/media/plugins/snt/snt-labkit-training.png | [Semantic segmentation](/plugins/snt/machine-learning)
 /media/plugins/snt/sholl-analysis-outputs.png | [Sholl](/plugins/snt/sholl) and [Strahler](/plugins/snt/analysis#strahler) directly from images (bypassing tracing)
 /media/plugins/snt/snt-angular-sholl.png | Advanced [Sholl-based quantifications](/plugins/snt/sholl#angular-sholl)
 /media/plugins/snt/snt-root-angle-analysis.png | [Root Angle Analysis](/plugins/snt/analysis#root-angle-analysis)
 /media/plugins/snt/snt-local-angle-surface-analysis.png | Analysis of [surface angles/arbor orientation](/plugins/snt/metrics#extension-angle)
-/media/plugins/snt/snt-delineation-analysis2.png | [Delineation analyses](/plugins/snt/walkthroughs#delineation-analysis)
 /media/plugins/snt/snt-growth-analysis.png | [Growth Analysis](/plugins/snt/analysis#growth-analysis)
+/media/plugins/snt/snt-delineation-analysis2.png | [Delineation analyses](/plugins/snt/walkthroughs#delineation-analysis)
 /media/plugins/snt/snt-ferris-wheel.png | Routines to summarize [innervation patterns](/plugins/snt/analysis#graph-based-analysis)
 /media/plugins/snt/graph-viewer-ferris-wheel.png | Routines to summarize data from [projectomes and connectomics](/plugins/snt/analysis#graph-based-analysis)
 /media/plugins/snt/snt-2d-histogram.png | Specialized [statistics](/plugins/snt/analysis#statistics)
-/media/plugins/snt/snt-labkit-training.png | [Semantic segmentation](/plugins/snt/machine-learning)
-/media/plugins/snt/snt-astrocyte-example.png | Glia analysis: Bulk characterization (width and length) of astrocytic processes ([use case](https://forum.image.sc/t/determining-astrocyte-width-from-2d-images-using-fiji-snt/56426/2))
+/media/plugins/snt/snt-delaunay-triangulation.png | Delaunay tessellation: Tracings can be used in [image processing routines](/plugins/snt/manual#process-)
+/media/plugins/snt/snt-density-map.png | Density maps for group(s) of cells obtained from [built-in scripts](/plugins/snt/scripting#bundled-templates)
+/media/plugins/snt/snt-recviewer-convexhull-and-surface.png | [Convex hulls](/plugins/snt/analysis#convex-hull-analysis) and [surface annotations](/plugins/snt/reconstruction-viewer#geometric-annotations)
+/media/plugins/snt/snt-montage-light.png | Quantitative and publication-quality visualizations
+/media/plugins/snt/snt-montage-dark.png | Rich 3D visualizations with dark theme
+/media/plugins/snt/snt-rec-viewer-demo2-dark.gif | [Interactive 3D scenes](/plugins/snt/reconstruction-viewer)
+/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-astrocyte-example.png | Glia analysis: Quantification of [astrocyte and microglia morphologies](./auto-tracing#multiple-cells)
 /media/plugins/snt/snt-non-neuronal-example.png | Not only neurons: SNT can be used to analyze many types of filamentous structures
 "
 %}

_pages/plugins/snt/index.md

@@ -54,7 +54,7 @@ The [Command Palette](manual#command-palette) ({% include key keys='ctlcmd|Shift
 | {% include key key='1' %} | Toggles the first visibility filter: Whether all traced paths should be displayed or just selected ones |
 | {% include key key='2' %} | Toggles the second visibility filter: Whether all nodes should be displayed across the Z-stack or just those in nearby Z-slices |
 | {% include key key='3' %} | Toggles the third visibility filter: Whether paths from all channels/frames should be displayed or just those in the active channel/frame |
-| {% include key key='G' %} | Selects the nearest path to the mouse cursor. Holding {% include key keys='Shift|G' %} adds the path nearest to the mouse cursor to the current list of selected paths. *Mnemonic: <u>G</u>rab paths around cursor.* Note that Paths can only be edited one at a time, and thus {% include key keys='Shift|G' %} is disabled in *Edit Mode* |
+| {% include key key='G' %} | <u>G</u>rabs the nearest path to the mouse cursor. Holding {% include key keys='Shift|G' %} adds the nearest path to the current selection. Note that Paths can only be edited one at a time, and thus {% include key keys='Shift|G' %} is disabled in *Edit Mode* |
 | {% include key key='H' %} | Temporarily <u>H</u>ides all paths/annotations while pressed |
 | {% include key key='O' %} | Temporarily shows path <u>O</u>rientations (start→end direction) while pressed |
 
@@ -87,9 +87,12 @@ These shortcuts become available in *Edit Mode*, activated through the contextua
 | {% include key key='I' %} | <u>I</u>nserts a new node at cursor position |
 | {% include key key='L' %} | <u>L</u>ocks active node to prevent accidental editing |
 | {% include key key='M' %} | <u>M</u>oves active node to cursor position |
+| {% include key key='P' %} | Toggle <u>P</u>aint Mode for brush editing |
 | {% 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 |
+| {% include key keys='Ctrl|Mouse Wheel' %}     | Adjust node radius / brush size (Paint Mode) |
+| {% include key keys='Alt|Drag' %}             | Move node / blend radii (Paint Mode) |
 
 ### Reconstruction Viewer
 

_pages/plugins/snt/key-shortcuts.md

@@ -152,23 +152,34 @@ Exits the program.
 
 ### 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...
+Runs fully automated tracing of a single cell directly from a **grayscale (intensity) image** already open in SNT (no binarization required). See [Autotracing › Grayscale Images](/plugins/snt/auto-tracing#grayscale-images) for details.
 
-#### Grayscale Image (GWDT) File...
+#### Grayscale Image (Multiple Cells)...
+Runs automated tracing of **multiple cells** in a single grayscale image. Automatically detects all soma locations, then traces each cell independently using exclusion masks to prevent territory overlap. See [Auto-tracing › Multiple Cells](/plugins/snt/auto-tracing#multiple-cells) for details.
 
-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(s)...
+Standalone tool for automatic soma/root detection in neuronal images, and can export results as a path node or ROI (point, contour, circle) for annotation or seeding autotracing. Options include:
 
-#### 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.
+- **Scope** Whether to detect only the single brightest/largest soma or all somata in the image. When detecting all somata, additional filtering parameters become available
+
+- **Output type** How results are exported: as a _Single-node path_ (for seeding autotracing), _Point ROI_, _Area ROI_ (contour from thresholding), or _Circular ROI_ (circle with EDT-derived radius)
+
+Remaining options are described in [Auto-tracing › Soma Detection](/plugins/snt/auto-tracing#soma-detection).
 
 #### 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.
 
+#### Grayscale Image File(s)...
+Batch-capable variant that loads grayscale images from a **file** or **directory**, traces a single cell per image using GWDT autotracing, and exports reconstructions as SWC files. See [Auto-tracing › Grayscale Images](/plugins/snt/auto-tracing#grayscale-images) and [Batch Processing](/plugins/snt/auto-tracing#batch-processing) for details.
+
+#### Grayscale Image File(s) (Multiple Cells)...
+Batch-capable variant that loads grayscale images from a **file too large to be loaded into memory** (e.g., an OME-ZARR, or .IMS file) or **directory**, detects all soma locations, and traces each cell independently using GWDT autotracing with exclusion masks. Results are exported as SWC files (one per detected cell). See [Auto-tracing › Multiple Cells](/plugins/snt/auto-tracing#multiple-cells) and [Batch Processing](/plugins/snt/auto-tracing#batch-processing) 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.
+Batch-capable variant that loads segmented images from a **directory**, traces each image, and exports the resulting reconstructions as SWC files. See [Auto-tracing › Segmented Images](/plugins/snt/auto-tracing#segmented-images) and [Batch Processing](/plugins/snt/auto-tracing#batch-processing) for details.
 
 
 ### Analysis ›
@@ -617,7 +628,7 @@ The status bar at the bottom of the Main Dialog displays brief messages about on
 Right-clicking on any of the tracing views will bring up a menu with various editing tools. The corresponding [keyboard shortcuts](/plugins/snt/key-shortcuts) are shown to the right of each option. The list includes:
 
 
-### Select Nearest Path {% include key key='G' %}
+### Grab Nearest Path {% include key key='G' %}
 Selects ("<u>G</u>roups") the path closest to the mouse cursor.
 
 ### Add Nearest Path to Selection {% include key key='Shift|G' %}
@@ -661,7 +672,7 @@ Removes the last segment from the temporary path.
 Finishes the temporary path. Note that a path can always be finished by {% include key key='double click' %}
 
 ## Edit Mode {% include key keys='Shift|E' %}
-Pressing *Edit Mode*, selects the nearest path for editing, unlocking the edit options. When *Edit Mode* is active, moving the mouse cursor along the path will highlight the nearest node with a crosshair icon and synchronize the current Z-slice to the location of that node. Note that the ability to create new paths is temporarily disabled when in *Edit Mode*.
+Pressing *Edit Mode*, selects the nearest path for editing, unlocking the edit options. When *Edit Mode* is active, moving the mouse cursor along the path will highlight the nearest node with a crosshair icon and synchronize the current Z-slice to the location of that node. Note that the ability to create new paths is temporarily disabled when in *Edit Mode*. For brush-based editing of multiple nodes at once, see [Paint Mode](#paint-mode-p) below.
 
 ### Bring Active Node to Current Z-plane {% include key key='B' %}
 Moves the active node to the active Z-plane. Note that the translation is only done in Z. XY positions are unchanged.
@@ -714,6 +725,22 @@ Reorganizes the existing tree so that the active node becomes its root.
 ### Split Tree at Active Node {% include key key='X' %}
 Splits the current tree into two subtrees by disconnecting the active node from its parent structure
 
+### Paint Mode {% include key key='P' %}
+Toggles Paint Mode, a brush-based sub-mode of Edit Mode for adjusting paths. In Paint Mode, operations fade smoothly from full effect at the cursor to no effect at the brush edge, like a soft brush in image editors. The brush radius (number of flanking nodes affected) is displayed in the status label.
+
+**{% include key keys='Drag' %}**  Moves nodes within the brush radius toward the cursor, weighted by proximity to the center node (Gaussian-like displacement)
+
+**{% include key keys='Alt|Drag' %}** Blends radii from the center node outward. Each flanking node's radius is pulled toward the center node's radius with fading falloff. Dashed arcs show the brush extent during the operation. 
+
+**{% include key keys='Ctrl|Mouse Wheel' %}** Adjusts the brush radius (number of flanking nodes). Transient dashed arcs preview the brush extent.
+
+Press {% include key key='P' %} again or exit Edit Mode to leave Paint Mode. Undo ({% include key key='Z' %}) reverts the last paint stroke.
+
+{% capture tip-paint%}
+Use {% include key key='R' %} to set the center node's radius first, then {% include key keys='Alt|Drag' %} to propagate it smoothly along the path.
+{% endcapture %}
+{% include notice icon="tip" content=tip-paint %}
+
 
 ## Pause Tracing {% include key keys='Shift|P' %}
 Disables tracing functions until this option is deselected. Tracing views are annotated with the *Tracing Paused* [label](#misc) to indicate this state.