Update snt manuals

Author: tferr

_pages/plugins/snt/manual.md

@@ -182,7 +182,7 @@ _Reconstruction Plotter_ is a whole-purpose 2D viewer for neuronal reconstructio
 - Can be combined in multi-panel viewers (mainly via scripting)
 
 #### Apply 3D Drift Corrections...
-A convenience alias for [Correct 3D Drift](/plugins/correct-3d-drift), which can correct abrupt displacements as well as slow drifts in video timelapses. It is recommended that you run _Correct 3D Drift_ on large time-lapse videos _before_ loading the image in SNT to avoid running out of RAM. See [Time-lapse analysis walkthrough](/plugins/snt/step-by-step-instructions#time-lapse-analysis) for details.
+A convenience wrapper for [Correct 3D Drift](/plugins/correct-3d-drift) that can correct abrupt displacements as well as slow drifts in video timelapses. See [Time-lapse analysis walkthrough](/plugins/snt/step-by-step-instructions#time-lapse-analysis) for details.
 
 
 #### Autotrace Segmented Image...

_pages/plugins/snt/scripting.md

@@ -21,7 +21,7 @@ SNT Scripts are intentionally written in multiple languages to demonstrate flexi
 
 ## Bundled Templates
 {% include img align="right" src="/media/plugins/snt/snt-scripts-menu.png" width="200px" caption="Scripts menu in main dialog"%}
-There are ~50 scripts currently bundled in SNT. These are organized into non-rigid categories: *Analysis* (typically handling quantifications) , *Batch* (Bulk processing of files), *Render* (visualization), *Skeletons & ROIs* (pixel-based analyses), *Tracing* (Tracing-related tasks), and *Demos*.
+There are 50+ scripts currently bundled in SNT. These are organized into non-rigid categories: *Analysis* (typically handling quantifications) , *Batch* (Bulk processing of files), *Render* (visualizations), *Skeletons & ROIs* (pixel-based analyses), *Tracing* (Tracing-related tasks), and *Demos* (teaching examples).
 
 Your script can also be bundled with SNT, or made available through the Neuroanatomy update site. Did you write a useful routine? Please [announce it](https://forum.image.sc/tag/snt), or submit a [pull request](https://github.com/morphonets/SNT/pulls) so that it can be distributed with Fiji!
 

_pages/plugins/snt/step-by-step-instructions.md

@@ -277,22 +277,29 @@ There are two demo datasets ({% include bc path='File|Load Demo Dataset...' %})
 {% endcapture %}
 {% include notice icon="info" content=timelapse-demo %}
 
-1. The first step is to ensure that the time-series is not affected by artifactual motion. Fiji features a host of registration tools to mitigate such artifacts. Arguably, one of the most intuitive of such tools is [Correct 3D Drift](/plugins/correct-3d-drift) because it can correct abrupt displacements as well as slow drifts. You can run it using [Apply 3D Drift Corrections...](/plugins/snt/manual#apply-3d-drift-corrections) if your image is small, but if your time-lapse video is rather large it is recommended that you run registration routines _before_ loading the image in SNT to avoid running out of RAM. The illustration below highligths the type of mitigation you should expect:
+{% include img align="right" name="Drift correction" src="/media/plugins/snt/snt-timelapse-drift-correction.png" caption="**Mitigation of motion artifacts**. Left: Projection of inter-frame differences across the original time-lapse sequence. Right: Inter-frame differences of the same time-lapse after 3D drift correction. Neurite displacements are color coded with warmer hues indicating higher motility. Note how lateral motion around the soma and along the longest extending neurite (lower left) has been minimized. Hue ramp has been scaled to the smallest (min) and largest (max) displacements in the sequence." %}
 
- {% include img align="center" name="Drift correction" src="/media/plugins/snt/snt-timelapse-drift-correction.png" caption="**Mitigation of motion artifacts**. Left: Projection of inter-frame differences across the original time-lapse sequence. Right: Inter-frame differences of the same time-lapse after 3D drift correction. Neurite displacements are color coded with warmer hues indicating higher motility. Note how lateral motion around the soma and along the longest extending neurite (lower left) has been minimized. Hue ramp has been scaled to the smallest (min) and largest (max) displacements in the sequence." %}
+The first step is to ensure that the time-series is not affected by artifactual motion. Fiji features a host of registration tools to mitigate such artifacts. Arguably, one of the most intuitive of such tools is [Correct 3D Drift](/plugins/correct-3d-drift) because it can correct abrupt displacements as well as slow drifts. 
 
-2. Specify the first time-point to be traced using the [Data Source](/plugins/snt/manual#data-source) widget
+SNT features [Apply 3D Drift Corrections...](/plugins/snt/manual#apply-3d-drift-corrections), a convenience wrapper for _Correct 3D Drift_ that applies drift correction to the image being traced, as well existing paths. However, if your time-lapse video is rather large it is recommended that you run _Correct 3D Drift_ (or alternative registration routine) _before_ loading the image in SNT to avoid running out of RAM. The illustration below highligths the type of mitigation you should expect.
 
-3. Trace the path of interest. This can be done manually or perhaps automated via a script (see below)
 
-4. Repeat 1. and 2. for all the frames to be traced. There are a couple of ways to expedite tracing across frames:
+Once undesired motion has been mitigated:
+
+
+1. Specify the first time-point to be traced using the [Data Source](/plugins/snt/manual#data-source) widget
+
+2. Trace the path of interest. This can be done manually or perhaps automated via a script (see below)
+
+3. Repeat 1. and 2. for all the frames to be traced. There are a couple of ways to expedite tracing across frames:
 
    - Duplicate the path(s) of interest using Path Manager's {% include bc path='Edit|[Duplicate...](/plugins/snt/manual#duplicate)' %} This will allow you to copy a path (and its children) to a new frame (or channel). If a neurite is retracting, you can duplicate the subsection of the path that better matches the retracted neurite: e.g., by restricting the duplication to a fraction of the path's total length, or up to a branch-point
 
    - Use a script to attempt segmentation at each frame, as in the _Segmented video (2D timelapse)_ demo ({% include bc path='File|Load Demo Dataset...' %})
-   <img align="right" src="/media/plugins/snt/snt-match-paths-across-time.png" title="MatchPath(s) Across Time... prompt" width="350" alt="MatchPath(s) Across Time... prompt" />
 
-5. Run Path Manager's {% include bc path='Analyze|Time-lapse Utilities|Match Path(s) Across Time...' %}. The dialog allows you to match paths in the same time-series to a common neurite. Note that the command matches only selected path(s) (or all paths if no selection exists), but ignores Paths tagged as 'soma'. Options include:
+4. Run Path Manager's {% include bc path='Analyze|Time-lapse Utilities|Match Path(s) Across Time...' %}. The dialog allows you to match paths in the same time-series to a common neurite. Note that the command matches only selected path(s) (or all paths if no selection exists), but ignores Paths tagged as 'soma'. Options include:
+
+   <img align="right" src="/media/plugins/snt/snt-match-paths-across-time.png" title="MatchPath(s) Across Time... prompt" width="350" alt="MatchPath(s) Across Time... prompt" />
 
     - **Frame range** Only paths associated with these frames will be considered for matching. Range(s) (e.g. <tt>2-14</tt>), and comma-separated list(s) (e.g. <tt>1,3,20,22</tt>) are accepted. Leave empty or type <tt>all</tt> to consider all frames
 
@@ -308,7 +315,7 @@ There are two demo datasets ({% include bc path='File|Load Demo Dataset...' %})
 
     - NB: Note that any mistakes by the matching algorithm can be corrected by editing _neurite#_ tags manually
 
-6. Once paths have been matched across the time-lapse to common neurites, future analysis becomes simplified. {% include bc path='Analyze|Time-lapse Utilities|Time Profile...' %} can be used to e.g. plot growth across time. {% include bc path='Time Profile...' %} includes the following options:
+5. Once paths have been matched across the time-lapse to common neurites, future analysis becomes simplified. {% include bc path='Analyze|Time-lapse Utilities|Time Profile...' %} can be used to e.g. plot growth across time. {% include bc path='Time Profile...' %} includes the following options:
 
       - **Metric** the measurement to be profiled across time