Merge pull request #384 from imagej/snt-release

Document Angular Sholl & BVV integration

Author: tferr

_pages/plugins/snt/analysis.md

@@ -242,7 +242,7 @@ Delineations allow measuring proportions of reconstructions within other structu
 Delineations are described in [Walkthroughs › Delineation Analysis](/plugins/snt/walkthroughs#delineation-analysis).
 
 # Root Angle Analysis
-Root angle analysis measures the angular distribution of how far neurites deviate from a direct path to the soma (or root of the neuronal arbor), a functional property that is captured by [Sholl profiles](#sholl-analysis). It quantifies properties such as [balancing factor](./metrics#root-angles-balancing-factor), [centripetal bias](./metrics#root-angles-centripetal-bias), and [mean direction](./metrics#root-angles-mean-direction). It is described in:
+Root angle analysis measures the angular distribution of how far neurites deviate from a direct path to the soma (or root of the neuronal arbor), a functional property that is captured by [Sholl profiles](#sholl-analysis) (see also [angular Sholl](./sholl#angular-sholl)). It quantifies properties such as [balancing factor](./metrics#root-angles-balancing-factor), [centripetal bias](./metrics#root-angles-centripetal-bias), and [mean direction](./metrics#root-angles-mean-direction). It is described in:
 
 {% include citation doi='10.1016/j.celrep.2019.04.097' %}
 
@@ -263,6 +263,11 @@ The analysis can be performed from the [Analysis menu](/plugins/snt/manual#root-
 
 Growth Analysis provides detailed time-lapse analysis of neuronal  patterns and requires traced paths to be matches across time frames, as detailed in. The Analysis is accessed through the [Path Manager](./manual#path-manager)'s [Time-lapse Utilities](./manual#time-lapse-utilities-) menu.
 
+{% capture timelapse-demo%}
+For parameter validation and configuration comparisons, load the _Hippocampal neuron (DIC timelapse)_ demo dataset ({% include bc path='File|Load Demo Dataset...' %})
+{% endcapture %}
+{% include notice icon="info" content=timelapse-demo %}
+
 ## Prerequisites
 
 - **Time-matched paths**: Paths must be tagged using the {% include bc path='Match Paths Across Time...'%} command first, so that all paths in the timelapse sequence associated with the same neurite are tagged with a common neurite label, e.g., "{neurite #1}", "{neurite #2}", etc, as described in the [Time-lapse analysis](./walkthroughs#time-lapse-analysis) walkthrough.

_pages/plugins/snt/big-data.md

@@ -0,0 +1,25 @@
+---
+title: SNT › Big Data
+nav-links: true
+nav-title: Big Data
+artifact: org.morphonets:SNT
+icon: /media/icons/snt.png
+forum-tag: snt
+update-site: Neuroanatomy
+tags: snt,tracing,segmentation,neuroanatomy,big-data
+---
+
+{% capture version%}
+**This page was last revised for [version 5.0.0](https://github.com/morphonets/SNT/releases)**.
+{% endcapture %}
+{% include notice content=version %}
+
+## Big Data support
+
+SNTv5 implemented _preliminary_ support for big data. The support remains basic but currently supports the following operations:
+
+| Operation          | Status                | Details |
+|--------------------|-----------------------|---------|
+| Tracing operations | Headless support only | A* tracing performed using pre-existing coordinates is fully supported via scripting in headless operations. [Example implementation](https://github.com/AllenNeuralDynamics/neuron-tracing-utils). For interactive tracing, please use [HortaCloud](https://hortacloud.org/): This is SNT's development team recommended tool for tracing Terabyte-size datasets |
+| Path optimization  | Headless support only | [Optimization of curvatures](./manual#refinefit-), including extraction of radii |
+| 3D Visualization   | Supported via [sciview](./manual#sciview) and [BigVolumeViewer](./manual#bigvolumeviewer)  | Visualization of 3D reconstructions, including [color mappings](./manual#color-mapping-), etc. |

_pages/plugins/snt/comp-tools.md

@@ -13,15 +13,16 @@ update-site: Neuroanatomy
 | Tool | Description | Comments |
 |------|-------------|----------|
 | [Spot Spine](/plugins/spot-spine) | Detection and count dendritic spines, segmentation of spine heads, and quantitative morphological measurements of spines | Under active development |
-| [BigTrace](/plugins/bigtrace) | Semi-automated tracing in 3D using BigVolumeViewer | Under active development |
+| [BigTrace](/plugins/bigtrace) | Semi-automated/automated tracing of unbranched structures using BigVolumeViewer | Under active development |
 | [NeuronJ](/plugins/neuronj) | Semi-automated tracing in 2D only | No longer maintained. SNT reads NDF files |
 
 
 ### Other
 
 | Tool | Description |
 |------|-------------|
-| [HortaCloud](https://hortacloud.org/) | Cloud-based, open-source platform for collaborative reconstruction of long-range projection neurons from whole-brain light microscopy data |
+| [HortaCloud](https://hortacloud.org/) | Cloud-based, open-source platform for collaborative reconstruction of long-range projection neurons from whole-brain light microscopy data. This is SNT's development team recommended tool for tracing [Terabyte-size datasets](./big-data) |
+| | |
 | [BICCN Tools](https://biccn.org/tools) | List of tools supporting NIH's Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative - Cell Census Network (BICCN) |
 | [Blue Brain's Morphology Suite](https://github.com/BlueBrain/morphology-suite) | Blue brain's collection of tools (mostly Python) to build, analyze and visualize morphologies. Currently supported by the [Open Brain Institute](https://www.openbraininstitute.org/) |
 | [Cajal](https://cajal.readthedocs.io/en/latest/index.html#) | A Python package for the analysis of single-cell morphological data using  Gromov-Wasserstein (GW) distances |

_pages/plugins/snt/index.md

@@ -40,11 +40,12 @@ The [source repository](https://github.com/morphonets/SNT) contains more details
 /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/sholl-analysis-outputs.png | [Sholl](/plugins/snt/analysis#sholl-analysis) and [Strahler](/plugins/snt/analysis#strahler-analysis) analysis
-/media/plugins/snt/snt-delineation-analysis2.png | [Delineation analyses](/plugins/snt/walkthroughs#delineation-analysis)
+/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-root-angle-analysis.png | [Root Angle Analysis](/plugins/snt/analysis#root-angle-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)

_pages/plugins/snt/key-shortcuts.md

@@ -51,6 +51,7 @@ The [Command Palette](manual#command-palette) ({% include key keys='ctlcmd|Shift
 | {% 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>roup 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='H' %} | Temporarily <u>H</u>ides alls paths/annotations while being pressed |
 
 
 ### Tracing

_pages/plugins/snt/manual.md

@@ -477,7 +477,8 @@ This option assumes [sciview](/plugins/sciview) to be successfully installed. sc
 ### Big Volume Viewer
 
 Big Volume Viewer (BVV) is the 3D counterpart of [BigDataViewer](https://imagej.net/plugins/bdv) capable of GPU volume rendering of images too large to fit into memory. Currently, support for Big Volume Viewer remains highly experimental.
-    
+{% include img align="center" name="BVV integration" src="/media/plugins/snt/snt-bvv.png" caption="BVV integration" %}
+
 ### Legacy 3D Viewer
 
 The Legacy 3D Viewer is a functional tracing canvas and allows images to be traced interactively in 3D. However, it relies on libraries that are not actively maintained and _may_ not function reliably during complex tasks. That being said, SNTv5 has implemented several improvements that have restored/improved Legacy 3D Viewer functionality relatively to earlier versions. For usage instructions, see [Tracing using the Legacy 3D Viewer](/plugins/snt/walkthroughs#tracing-in-the-legacy-3d-viewer).