VolRoverN Tutorial

VolRoverN Tutorial


This tutorial walks the user through downloading, installing and running VolRoverN. It performs the tasks of loading volume data, loading contour data, fitting a surface to contours, segmentation and export to NEURON and MCell software packages. It is targeted for the Mac OS X platform.

All data is relative to the sample directory distributed with VolRoverN.

Download and install

Process data

FAQ

Download and install

Download VolRoverN at this link. Unpack. Also download the sample data available on the same page.

Process data

  1. Open VolRoverN
  2. Open a volume
    1. File > Open
    2. Change the filter to “Volume”
    3. Choose file volume.cvc and click Open
    4. The volume will show up in the viewer when open
    5. See this FAQ entry if the left viewer window doesn’t show anything
  3. Open contour files
    1. File > Open
    2. Change the filter to “Reconstruct series”
    3. Choose file traces/traces.ser and click Open
    4. See this FAQ entry to see how to determine when the contours are loaded.
  4. Open Volume Grid Rover
    1. View > Show Volume Grid Rover
    2. In the bottom-middle of the Volume Grid Rover window, uncheck and then check “Grey Scale Density Map”
    3. You can zoom in and out and pan the image shown.
    4. Contours are initially shown in red. To change the color of a given contour, highlight it in the list on the “Grid Cell Marking > Contours” tab and click the red button. Check and uncheck the “Render points” box to show and hide polygon vertices.
    5. Return to the VolRoverN main window
  5. Tile (e.g. fit a surface to) the contours for axon a001
    1. Tools > Contour Tiler
    2. Select component “a001″
    3. Accept all defaults and click OK
    4. A message at the bottom of the window will tell you when tiling is complete.
    5. The tiled axon is initially obscured by the volume. Move the “Near Clip Plane” slider to the right until you see the axon.
    6. File > Save
      1. Select a001
      2. Enter a001 for the Output Filename
      3. Click OK. The reconstructed surface is now saved to disk.
  6. Check correctness:
    1. Click on the Data tab
    2. In the Object Key column, click on the loaded geometry
    3. On the right of the screen you’ll see information about the geometry
    4. Click on the Find problems button
    5. If there holes or non-manifold areas, dismiss the window and click
      on Fix problems

    6. After fixing problems, click once more on Find problems to confirm
  7. Consider the following viewing options:
    1. View > Viewer properties to see a list of geometries loaded in the zoom window. Check or uncheck each one to determine visibility.
    2. To see the quality of triangles of the surface, View > Filled wireframe
    3. View > Clip Geometry to Bounding Box to toggle clipping of the geometry to the zoom window view box
    4. View > View Wire Cube to toggle visibility of the wire cube in the zoom window
  8. Improve triangle quality
    1. Choose Tools > Surface simplification to reduce the number of triangles using the qslim algorithm. Accept all defaults.
    2. Choose Tools > LBIE Quality Improvement to improve triangle quality
      1. Select a001-dec as the surface
      2. Change “Iterations” to 1
      3. After completion, uncheck “a001-dec” and check “a001-dec_LBIE_imp” in the “Viewer properties” window
  9. Export single axon to NEURON
    1. Choose Tools > Cable model
    2. Uncheck everything except for “a001-dec_LBIE_imp”
    3. Click OK
    4. Upon completion, uncheck “a001-dec_LBIE_imp” in the “Viewer properties” window
    5. Hold down the shift key and click on a colored region to see the region’s unique ID displayed at the bottom of the main window
    6. Go to Finder and load a001-dec_LBIE_imp.hoc in a text editor. It is ready to be loaded into NEURON with a default integrate command.
  10. Export a dendrite, axon and synapse to NEURON
    1. Tile dendrite d001 (see the Tile step)
    2. Decimate d001 to 20000 triangles using Tools > Surface Simplification. Do not decimate to anything lower than 20000 triangles since this will result in non-manifoldness due to the narrow spine necks.
    3. Triangle improve d001-dec using Tools > LBIE Quality Improvement
    4. Choose Cable model and choose d001-dec_LBIE_imp with 100 segments
    5. Find two regions (one in a001, one in d001) that likely have a synapse by holding down shift and clicking on the colored regions. Regions 21 (in a001) and 65 (in d001) are candidates.
    6. Choose Tools > Hoc Merge.
      1. Enter 21 for a001 and 65 for d001
      2. Click OK
      3. Go to Finder and load merged.hoc in a text editor. It is ready to be loaded into NEURON with a default command.
  11. Export to MCell
    1. Export an axon to NEURON
    2. Choose Tools > MCell Export
    3. Uncheck everything except “a001-dec_LBIE_imp-ssurf”
    4. Click OK

FAQ

The left viewer window doesn’t show my data.
Occasionally the zoom level in the left viewer window (zoomed window) isn’t quite right. If, after opening data files, nothing shows up in your zoomed window then simply zoom out until you see the data.

I started a process but don’t know if it’s done or not.
Some processes in VolRoverN rely on the Threads and Log tabs for feedback. To see if your command is complete or not, click on the Threads tab. If there is an entry corresponding to your command, then it is currently running. It is complete when the entry is removed. If you wish to see log feedback of your task, click on the Log tab. Many commands will give a message in the bottom-left of the main window when complete.