SNT: FAQ

Revision as of 15:30, 18 May 2019 by Tiago (talk | contribs) (WIP: SWC vs TRACES)
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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...


General

  1. What is a SWC file?
  2. 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.
  3. In which format should I save my tracings: TRACES or SWC?
  4. 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 ›   provides a batch converter for TRACESSWC conversion. The following table summarizes the differences between the two formats:
    SWC TRACES
    No. reconstructions / file Only one. When multiple reconstructions exits, SNT splits them across multiple files appending unique suffixes to filenames Multiple reconstructions per file allowed
    Image metadata Only spatial calibration Stored. 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 Exlusive to SNT. But open and easily parsable
  5. How can I improve SNT documentation?
  6. 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!
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