Difference between revisions of "SNT: FAQ"

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== General ==
== Tracing ==
 
 
<ol>
 
<ol>
 
<li>
 
<li>
<span id="confirmtemp"></span>'''Having to confirm indivual segments is too cumbersome for me. Is it possible to  trace without interruption, by clicking in succession'''?
+
<span id="install"></span>'''How do I install SNT'''?
 
</li>
 
</li>
 
<dl><dd>
 
<dl><dd>
Yes. Uncheck the ''Confirm temporary segments'' in the ''Options'' tab (''Temporay Paths'' section).
+
        See [[#SNT#Installation|Installation details]].
 
</dd></dl>
 
</dd></dl>
 
<li>
 
<li>
<span id="intensities"></span>'''How can I browse voxel intensities around processes'''?
+
<span id="citing"></span>'''How do I cite SNT'''?
 
</li>
 
</li>
 
<dl><dd>
 
<dl><dd>
Righ-click on the image canvas and select ''Pause SNT'' from the contextual menu. Voxel intensities will be reported in the ImageJ status bar.
+
SNT is based on multiple publications. To cite SNT:
 +
* Ferreira T, et al. ('''2019''') (TBD)
 +
To reference other plugins that enhance SNT:
 +
* '''[[Sholl Analysis]]''': Ferreira T, Blackman A, Oyrer J, Jayabal A, Chung A, Watt A, Sjöström J, van Meyel D. ('''2014'''), [http://www.nature.com/nmeth/journal/v11/n10/full/nmeth.3125.html Neuronal morphometry directly from bitmap images], ''Nature Methods'' 11(10): 982–984
 +
* '''[[SNT: Tubular Geodesics|Tubular Geodesics]]''': Türetken E, Benmansour F, Fua P. [https://infoscience.epfl.ch/record/176222/files/turetken_et_al_2012.pdf?version=1 Automated Reconstruction of Tree Structures using Path Classifiers and Mixed Integer Programming]. <i>IEEE Conference on Computer Vision and Pattern Recognition</i>, Providence, Rhode Island, 2012.
 +
The original [[#snt|Simple Neurite Tracer]] publication is:
 +
* Longair MH, Baker DA, Armstrong JD. [http://bioinformatics.oxfordjournals.org/content/early/2011/07/04/bioinformatics.btr390.long Simple Neurite Tracer: Open Source software for reconstruction, visualization and analysis of neuronal processes]. <i>Bioinformatics</i> 2011
 
</dd></dl>
 
</dd></dl>
 
<li>
 
<li>
<span id="groupimages"></span>'''Is there a way to process one image after another in a fast way'''?
+
<span id="snt"></span>'''What is the difference between SNT and Simple Neurite Tracer'''?
 
</li>
 
</li>
 
<dl><dd>
 
<dl><dd>
Yes. Have a look at these [https://forum.image.sc/t/simple-neurite-tracer-for-multiple-2d-images/22564/6?u=tferr detailed instructions].
+
Simple Neurite Tracer was the first Fiji plugin dedicated to visualization and reconstruction of neurons, developed by [[User:Mark|Mark Longair]] and [[#citing|published in 2011]], to become the single most cited open-source software for semi-automated 3D reconstructions. In the wake of ImageJ2 development, a new team of developers lead by [[User:Tiago|Tiago Ferreira]] took on the effort of modernizing its code base. The project quickly snowballed beyond the re-write of the software, and focused on establishing a complete framework for reconstruction, visualization, quantification and modelling of neuronal morphology. Several name changes were proposed for this "next-gen" Simple Neurite Tracer (''Not so Simple Neurite Tracer'', ''Smart Neurite Tracer'', ''Super Neurite Tracer'' to name a few), but in the end it was decided to adopt the acronym of the original software, as an homage to Mark's outstanding work. You can follow the entire history of the plugin on GitHub:  Simple Neurite Tracer's {{GitHub|org=fiji|repo=Simple_Neurite_Tracer|label=historic}}  and SNT's {{GitHub|org=morphonets|repo=SNT|label=current}} repositories.
 
</dd></dl>
 
</dd></dl>
 
<li>
 
<li>
<span id="imageseq"></span>'''How can I import an image sequence into SNT'''?
+
<span id="accuracy"></span>'''How accurate is SNT'''?
 
</li>
 
</li>
 
<dl><dd>
 
<dl><dd>
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 {{bc|color=white|File| Import|Image Sequence}} 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 {{bc|color=white|Image|Properties...}}. To save yourself from having to go through these steps again, you should save the imported stack as a single TIFF file using {{bc|color=white|File|Save As|Tiff...}}
+
When SNT is compiled, a [https://github.com/morphonets/SNT/tree/master/src/test/java/sc/fiji/snt suite of tests] is run to detect deficiencies in the code base. Morphometry results are benchmarked against values obtained in [http://cng.gmu.edu:8080/Lm/ L-Measure] and [https://github.com/BlueBrain/NeuroM NeuroM]. However, no test suite is ever perfect. If you detect inaccuracies, please {{GitHub|org=morphonets|repo=SNT|label=report}} them!
 
</dd></dl>
 
</dd></dl>
</ol>
 
 
 
 
== General ==
 
<ol>
 
 
<li>
 
<li>
 
<span id="swc"></span>'''What is a SWC file'''?
 
<span id="swc"></span>'''What is a SWC file'''?
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</li>
 
</li>
 
<dl><dd>
 
<dl><dd>
When tracing 4D or 5D images, <tt>TRACES</tt> is preferable because the channel and/or time frame associated with the data are stored. With simpler 2/3D images <tt>TRACES</tt> is also preferable to preserve [[SNT:_Overview#Tag|Path Manager tags]] across restarts. Note that the {{bc|[[SNT:_Overview#Scripts|Scripts]]|&nbsp;}} provides a batch converter for  <tt>TRACES</tt> &rarr; <tt>SWC</tt>  conversion. The following table summarizes the differences between the two formats:
+
When tracing 4D or 5D images, <tt>TRACES</tt> is preferable because the channel and/or time frame associated with the data are stored. With simpler 2/3D images <tt>TRACES</tt> is also preferable to preserve [[SNT:_Overview#Tag|Path Manager tags]] across restarts. Note that the {{bc|[[SNT:_Overview#Scripts|Scripts]]|&nbsp;}} menu provides a [[#convert|batch converter]] for  <tt>TRACES</tt> &rarr; <tt>SWC</tt>  conversion. The following table summarizes the differences between the two formats:
 
{| class="wikitable" style="width: 100%"|
 
{| class="wikitable" style="width: 100%"|
 
!  
 
!  
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|-
 
|-
 
| style="width: 20%"| No. reconstructions / file
 
| style="width: 20%"| No. reconstructions / file
| style="width: 40%"| Only one. When multiple reconstructions exits, SNT splits them across multiple files appending unique suffixes to filenames
+
| style="width: 40%"| Formally only one. When multiple reconstructions exits, SNT splits them across multiple files appending unique suffixes to filenames
| style="width: 40%"| Multiple reconstructions per file allowed
+
| style="width: 40%"| Multiple reconstructions per file allowed
 
|-
 
|-
 
| Image metadata
 
| Image metadata
| Only spatial calibration
+
| Formally none. SNT stores the spatial calibration of the image in the header
| Stored. Including channel and frame of the traced structure
+
| Rich. Including channel and frame of the traced structure.
 
|-
 
|-
 
| [[SNT:_Overview#Tag|Path Manager tags]]
 
| [[SNT:_Overview#Tag|Path Manager tags]]
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|-
 
|-
 
| Presence
 
| Presence
| Ubiquitous among reconstruction software
+
| Ubiquitous among reconstruction software. The ''de facto'' standard in data sharing
 
| Exlusive to SNT. But [[SNT:_.traces_File_Format|open and easily parsable]]
 
| Exlusive to SNT. But [[SNT:_.traces_File_Format|open and easily parsable]]
 
|}
 
|}
 +
</dd></dl>
 +
<li>
 +
<span id="convert"></span>'''How do I (batch) convert TRACES to SWC'''?
 +
</li>
 +
<dl><dd>
 +
        In the [[Script Editor]] ({{bc|File|New|Script...}}) look for {{bc|Templates|Neuroanatomy|Batch|Convert Traces to SWC}} and run it. Note that all of SNT scripts are also listed in the main as regular GUI commands in the main [[SNT:_Scripting#Script_Templates|interface]]. Don't see the scripts? Please ensure SNT is  properly [[SNT#Installation|installed]].
 
</dd></dl>
 
</dd></dl>
 
<li>
 
<li>
Line 77: Line 82:
 
</dd></dl>
 
</dd></dl>
 
</ol>
 
</ol>
 +
 +
 +
== Tracing ==
 +
<ol>
 +
<li>
 +
<span id="confirmtemp"></span>'''Having to confirm indivual segments is too cumbersome for me. Is it possible to  trace without interruption, by clicking in succession'''?
 +
</li>
 +
<dl><dd>
 +
Yes. Uncheck the ''Confirm temporary segments'' in the ''Options'' tab (''Temporay Paths'' section).
 +
</dd></dl>
 +
<li>
 +
<span id="intensities"></span>'''How can I browse voxel intensities around processes'''?
 +
</li>
 +
<dl><dd>
 +
Righ-click on the image canvas and select ''Pause SNT'' from the contextual menu. Voxel intensities will be reported in the ImageJ status bar.
 +
</dd></dl>
 +
<li>
 +
<span id="groupimages"></span>'''Is there a way to process one image after another in a fast way'''?
 +
</li>
 +
<dl><dd>
 +
Yes. Have a look at these [https://forum.image.sc/t/simple-neurite-tracer-for-multiple-2d-images/22564/6?u=tferr detailed instructions].
 +
</dd></dl>
 +
<li>
 +
<span id="imageseq"></span>'''How can I import an image sequence into SNT'''?
 +
</li>
 +
<dl><dd>
 +
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 {{bc|color=white|File| Import|Image Sequence}} 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 {{bc|color=white|Image|Properties...}}. To save yourself from having to go through these steps again, you should save the imported stack as a single TIFF file using {{bc|color=white|File|Save As|Tiff...}}
 +
</dd></dl>
 +
</ol>
 +
  
 
{{SNTNavBar}}
 
{{SNTNavBar}}

Latest revision as of 07:59, 31 May 2020

Home Manual Walk-throughs Screencasts Shortcuts Rec. Viewer Analysis Scripting Modeling FAQ



General

  1. How do I install SNT?
  2. See Installation details.
  3. How do I cite SNT?
  4. SNT is based on multiple publications. To cite SNT:
    • Ferreira T, et al. (2019) (TBD)
    To reference other plugins that enhance SNT: The original Simple Neurite Tracer publication is:
  5. What is the difference between SNT and Simple Neurite Tracer?
  6. Simple Neurite Tracer was the first Fiji plugin dedicated to visualization and reconstruction of neurons, developed by Mark Longair and published in 2011, to become the single most cited open-source software for semi-automated 3D reconstructions. In the wake of ImageJ2 development, a new team of developers lead by Tiago Ferreira took on the effort of modernizing its code base. The project quickly snowballed beyond the re-write of the software, and focused on establishing a complete framework for reconstruction, visualization, quantification and modelling of neuronal morphology. Several name changes were proposed for this "next-gen" Simple Neurite Tracer (Not so Simple Neurite Tracer, Smart Neurite Tracer, Super Neurite Tracer to name a few), but in the end it was decided to adopt the acronym of the original software, as an homage to Mark's outstanding work. You can follow the entire history of the plugin on GitHub: Simple Neurite Tracer's historic and SNT's current repositories.
  7. How accurate is SNT?
  8. When SNT is compiled, a suite of tests is run to detect deficiencies in the code base. Morphometry results are benchmarked against values obtained in L-Measure and NeuroM. However, no test suite is ever perfect. If you detect inaccuracies, please report them!
  9. What is a SWC file?
  10. It is the most widely adopted format for encoding neuronal reconstructions, in which information is stored in plain text. It was first described by (Cannon et al., 1998) and since then became a somewhat loose lingua franca of a neuron's three dimensional structure. It is described in more detail here and here. SNT supports all known variants of the format including ESWC and SWC+. The extension stems from the last names of Stockley, Wheal, and Cole, who developed a neat computer system for reconstructing neuronal cells ( Stockley et al., 1993). Confusingly, it is also a deprecated file format used by Adobe.
  11. In which format should I save my tracings: TRACES or SWC?
  12. When tracing 4D or 5D images, TRACES is preferable because the channel and/or time frame associated with the data are stored. With simpler 2/3D images TRACES is also preferable to preserve Path Manager tags across restarts. Note that the Scripts ›   menu provides a batch converter for TRACESSWC conversion. The following table summarizes the differences between the two formats:
    SWC TRACES
    No. reconstructions / file Formally only one. When multiple reconstructions exits, SNT splits them across multiple files appending unique suffixes to filenames Multiple reconstructions per file allowed
    Image metadata Formally none. SNT stores the spatial calibration of the image in the header Rich. Including channel and frame of the traced structure.
    Path Manager tags Not stored Stored
    Format Plain text XML or compressed XML (as per preferences)
    Presence Ubiquitous among reconstruction software. The de facto standard in data sharing Exlusive to SNT. But open and easily parsable
  13. How do I (batch) convert TRACES to SWC?
  14. In the Script Editor (File › New › Script...) look for Templates › Neuroanatomy › Batch › Convert Traces to SWC and run it. Note that all of SNT scripts are also listed in the main as regular GUI commands in the main interface. Don't see the scripts? Please ensure SNT is properly installed.
  15. How can I improve SNT documentation?
  16. Create an account on this wiki. Once you have created one, you can edit contents at will. Don't be shy. All changes are undoable!


Tracing

  1. Having to confirm indivual segments is too cumbersome for me. Is it possible to trace without interruption, by clicking in succession?
  2. Yes. Uncheck the Confirm temporary segments in the Options tab (Temporay Paths section).
  3. How can I browse voxel intensities around processes?
  4. Righ-click on the image canvas and select Pause SNT from the contextual menu. Voxel intensities will be reported in the ImageJ status bar.
  5. Is there a way to process one image after another in a fast way?
  6. Yes. Have a look at these detailed instructions.
  7. How can I import an image sequence into SNT?
  8. 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 File ▷ Import ▷ Image Sequence 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 Image ▷ Properties.... To save yourself from having to go through these steps again, you should save the imported stack as a single TIFF file using File ▷ Save As ▷ Tiff...


Home Manual Walk-throughs Screencasts Shortcuts Rec. Viewer Analysis Scripting Modeling FAQ