The SWC Mesher add-on can create both 3D centerline (stick figure) and 3D mesh representations of neurons from SWC files. The meshes produced may be used directly with CellBlender or further improved with tools like GAMer.
SWC files (Stockley-Wheal-Cannon, Cannon et al., 1998) are available from a number of sources including neuromorpho.org. SWC file format is described in a FAQ available at http://neuromorpho.org/myfaq.jsp (reproduced here).
Q: What is SWC format?
A: The three dimensional structure of a neuron can be represented in a SWC format (Cannon et al., 1998).
SWC is a simple Standardized format. Each line has 7 fields encoding data for a single neuronal compartment:
* an integer number as compartment identifier
* type of neuronal compartment
0 - undefined
1 - soma
2 - axon
3 - basal dendrite
4 - apical dendrite
* x coordinate of the compartment
* y coordinate of the compartment
* z coordinate of the compartment
* radius of the compartment
* parent compartment
Every compartment has only one parent and the parent compartment for the first point in each file is
always -1 (if the file does not include the soma information then the originating point of the tree will
be connected to a parent of -1). The index for parent compartments are always less than child compartments.
Loops and unconnected branches are excluded. All trees should originate from the soma and have parent
type 1 if the file includes soma information. Soma can be a single point or more than one point. When the
soma is encoded as one line in the SWC, it is interpreted as a "sphere". When it is encoded by more than 1 line,
it could be a set of tapering cylinders (as in some pyramidal cells) or even a 2D projected contour ("circumference").
Start by enabling the add-on using the File/User Preferences menu and selecting the Add Mesh section and checking the box for the SWC Mesher add-on.
Select the "SWC Mesher" tab along the left side of the 3D View:
Start by opening the Import Cable Model from SWC File subpanel and use the file navigator to select an SWC format file:
Navagate to an SWC file. In this example we'll use the P40-DEV360.CNG.swc file (available at http://neuromorpho.org/neuron_info.jsp?neuron_name=P40-DEV360). The file is reproduced here (copy and save as a text file for testing):
# SWC to SWC conversion from L-Measure. Sridevi Polavaram: [email protected]
# Original fileName:/cng_repository/Soumya/LM_Automated_Testing_Enviornment/Test_Lm3.7.2_10062011_SG_Linux_NMOConv6/TestResults/LoadTest/test_10/P40-DEV360.CNG.swc
#
# Original file P40_DEV360.swc edited by Duncan Donohue using StdSwc version 1.31 on 2/27/08.
# Irregularities and fixes documented in P40_DEV360.swc.std. See StdSwc1.31.doc for more information.
#
# Neurolucida to SWC conversion from L-Measure. R. Scorcioni: [email protected]
# Original fileName:C:\Users\Duncan\Desktop\Dat files to convert\Furtak 181 asc\P40_DEV360.ASC
#
1 1 -0.78 -0.33 0 2.52262 -1
2 1 -0.78 2.18 0 2.52262 1
3 1 -0.78 -2.85 0 2.52262 1
4 3 0 1.67 2.12 0.67 1
5 3 0 4.68 2.12 0.67 4
6 3 3.35 6.69 2.12 0.67 5
7 3 3.35 9.02 2.12 0.67 6
8 3 3.68 9.69 2.12 0.67 7
9 3 4.01 10.37 2.12 0.67 8
10 3 -0.33 8.69 2.12 0.67 5
11 3 1.34 0.33 2.12 0.67 1
12 3 2.34 0.33 2.12 0.67 11
13 3 2.68 0.67 2.12 0.67 12
14 3 3.35 1 2.12 0.67 13
15 3 6.36 1 2.12 0.67 14
16 3 6.69 1.34 2.12 0.67 15
17 3 -0.67 -2.68 2.12 0.67 1
18 3 3.35 -4.68 2.12 0.67 17
19 3 4.85 -4.01 2.12 0.67 18
20 3 6.36 -3.35 2.12 0.67 19
21 3 6.69 -6.36 2.12 0.67 19
22 3 3.68 -8.36 2.12 0.67 18
23 3 -1.34 -2.34 2.12 0.67 1
24 3 -1.34 -2 2.12 0.67 23
25 3 -1.34 -6.02 2.12 0.67 24
26 3 0 -10.03 2.12 0.67 25
27 3 -3.01 -10.03 2.12 0.67 25
28 3 -2.34 0.33 2.12 0.67 1
29 3 -5.01 0.67 2.12 0.67 28
30 3 -5.35 1 2.12 0.67 29
31 3 -5.69 1 2.12 0.67 30
32 3 -7.69 4.34 2.12 0.67 31
After opening that file, you should see an overview below the "Analyze File" button:
This shows that the file contains 32 non-comment lines, 31 segments, and 32 nodes. The largest radius of all nodes is 2.52, and the smallest is 0.67. The spatial extent of the neuron is contained within the X, Y, and Z ranges shown.
You can create a line mesh object in Blender from that file by clicking the "Make Cable Model from File" button as shown here:
The following panel shows the resultant cable model:
The second panel "Edit Cable Model" contains several tools to (1) edit the cable model, and (2) extrapolate a surface mesh from the cable. The cable model you are currently editing is the one that you have selected in the "List of Cable Models". To add cable models to this list, select the cable model and press the appropriate cable model in Blender and press the + button. Alternatively, use the - and X buttons to remove models from the edit list.
You can edit cable models directly in Blender. Extrapolate points, delete points, and make new edges using all the default Blender tools in edit mode. After editing the cable, the internal data model that is used by Blender to represent the cable must be updated. To do this, press the "Update Cable Model from Geometry" button - unfortunately, this cannot be done automatically. The internal data model must be updated for any edits to take effect. Note that this update does not provide feedback.
Also Note: editing the cable model such that it does not meet the criteria for being a correct cable model (e.g. is edited to contain a loop) will lead to errors.
An example of extrapolating points is shown in the following panels.
Remember to update the cable model's internal data model via the "Update Cable Model from Geometry" button after edits are finished!
The cable model is really a ball-and-stick model, in the sense that a radius is associated with each point. To edit these radii, press the "Make Spheres for each Vertex" button:
Use the "Show"/"Hide"/"Delete All" buttons to toggle the sphere's visibility. Use the scale tool (press "s") to edit the radii of different spheres. You may also move the spheres using the grab tool (press "g") to edit the geometry.
Remember to update the cable model's internal data model via the "Update Cable Model from Spheres" button after edits are finished, as shown below:
Note that this does not provide any feedback. The internal data model must be updated for any edits to take effect. To check that the data model has been updated correctly, press the "Delete All" button to delete all the spheres, and then again press the "Make Spheres for each Vertex" button.
You can edit multiple cable models by adding them to the "List of Cable Models" to edit. Follow the steps above in the "Import Cable Model from SWC File" panel to import a second SWC file. After importing, the new cable model will be automatically added to the list of cable models to edit. Alternatively, select the cable model in Blender, and use the + button to add the cable model:
The cable model that you are currently editing or extrapolating a surface mesh from is the one that is actively selected in the "List of Cable Models":
You can create a surface mesh object in Blender from that file by opening the "Surface Mesh" panel and clicking the "Make Surface Mesh from File" button as shown here:
As shown here, the add-on will create a series of "Meta" objects which form the surface of the Neuron. This isn't a mesh at this point, but can be easily converted to a mesh by selecting the object (right clicking to turn from dark orange to lighter "gold") and then using the menu commands (Object / Convert to / Mesh from Curve/Meta/Surf/Text) as shown here:
The result will typically look the same, but it will now be a mesh. You can see the mesh itself by entering "Edit" mode and zooming in:
To use the mesh with CellBlender, it will need to be triangulated. You can do this by selecting everything in edit mode (the "a" key - should turn the entire mesh bright orange), then use the menu to find Mesh/Faces/Trianguate Faces (or use control-t). The triangulated result for this model should have 30,128 vertices, 90,378 edges, and 60,252 faces.
This mesh can be used in CellBlender or MCell, but it has many more triangles than needed, and the geometry is often poor quality for simulation. There are a number of ways to improve the mesh, and the following picture shows the result of applying the Coarse Dense, Coarse Flat, and Smooth operators available in the Blender version of GAMER (https://github.com/mcellteam/gamer). Here's the final mesh:
The resulting Blender scene will contain both the outer mesh (shown unselected in black) and the original centerline (shown selected in orange):
The resulting mesh can be added to a CellBlender project as part of a simulation:
