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Saving the Spines

After you have detected all dendritic spines around the model, it is possible to save some of the information to a file. In lieu of a standardized file format for spines we have attempted to provide in this file as much information about individual spines as we can currently extract. The format and number of fields is expected to change as the program evolves.

To save the file select File >> Save Spines... from the menu. This brings up the standard windows save file dialog. Select the desired location for the file and hit OK.

This will create a simple text file as shown below. This text file can be opened in most text editors and spreadsheet programs. The fields can be parsed as spaced delimited records.

  ID  SECTION-NUMBER  SECTION-LENGTH    BRANCH-ORDER               X               Y               Z   HEAD-DIAMETER   NECK-DIAMETER         MAX-DTS            TYPE            AUTO   XYPLANE-ANGLE     SWC-NODE-ID SWC-NODE-OFFSET        ATTACH-X        ATTACH-Y        ATTACH-Z   SOMA-DISTANCE
   0               0       16.897375             N/A        8.135746        2.678505        8.075636        0.730371        0.010000        2.805931        mushroom             yes       28.173807               6        0.524068        5.623677        2.503094        9.424394        2.866865
   1               0       16.897375             N/A        5.775931        4.909771        5.758801        0.527911        0.010000        1.591411        mushroom             yes       32.530858              12        0.000000        4.625577        5.849836        6.706364        7.388226
   2               0       16.897375             N/A        4.129705        5.173902        9.761111        0.396513             N/A        1.537842          stubby             yes      -49.185402               9        0.000000        4.938086        4.321705        8.401009        5.076682
   3               0       16.897375             N/A        4.311893        2.188485       10.194888        0.567167        0.010000        1.411669        mushroom             yes      -25.006521               6        0.774907        5.697270        2.364781        9.543473        2.670074
   4               0       16.897375             N/A        4.222073        4.698213        9.382930        0.708078        0.586987        1.355815        mushroom             yes      -50.516097               9        0.000000        4.938086        4.321705        8.401009        5.076682
   5               0       16.897375             N/A        3.638982        8.875042        1.954092        0.746851             N/A        1.301612          stubby             yes       53.598929              20        0.407516        3.356438        9.660844        3.086688       12.899471
   6               0       16.897375             N/A        3.788573       11.076957        3.105673        0.290536        0.184380        0.922021            thin             yes      -23.241327              21        0.562138        3.093825       10.187087        2.620837       13.652308
   7               0       16.897375             N/A        3.888484       10.091292        3.815839        0.963377             N/A        0.831779          stubby             yes      -36.828272              20        0.745149        3.424533        9.470711        3.235590       12.648555
   8               0       16.897375             N/A        4.526393        8.190586        3.397809        0.670213             N/A        0.742180          stubby             yes       36.662445              18        0.653295        3.843264        8.578114        3.982423       11.373384
   9               0       16.897375             N/A        1.808397       11.282461        2.505427        0.601257             N/A        0.697419          stubby             yes      -43.687439              22        0.000000        2.348091       11.139782        1.972200       15.048719
 ...

Column Details

IMPORTANT: A value of N/A in any of the rows indicates that the value is not applicable for that spine.

ID: A unique identifier for each spine. These ID's are not guaranteed to be contiguous.

SECTION-NUMBER: The identifier of the section of the model where the spine attaches. The section numbers are unique and contiguous. See also Branch Order and Section Labels.

SECTION-LENGTH: The length of the section where the spine attaches. This length is the sum of the inter-vertex distances of all the vertices comprising the section. For example if the section is composed of 3 vertices A, B, and C, where the distance between A and B is 2.0 and the distance between B and C is 3.0, then the section length is 5.0.

BRANCH-ORDER: The branch order of the section of the model where the spine attaches. See also Branch Order and Section Labels.

X, Y, Z: The x,y,z coordinate of the center of mass of the spine.

HEAD-DIAMETER: The diameter of the head of the spine.

NECK-DIAMETER: The diameter of the neck of the spine.

MAX-DTS: The distance from the "tip" of the spine to the surface of the model. This value is therefore an approximate measure of the length of the spine. Note that the tip is the voxel contained within the spine that is furthest from the surface.

TYPE: The class of the spine. Possible values are currently stubby, thin, mushroom, or other.

AUTO: A yes or no value indicating whether the spine was found by running the automatic spine detection, or manually by the user.

XYPLANE-ANGLE: The angle formed between the approximate medial axis of the spine and the XY plane. This value gives a measure of the directionality of the spine as compared to the optical axis.

SWC-NODE-ID, SWC-NODE-OFFSET: These two values together give a means for mapping the attachment point of the spine onto the medial axis of the model saved in SWC format. The ID gives the SWC label of the node where the spine is near. The offset gives how far along the edge between that node and its parent node the spine attaches. A value of 0.0 for the offset indicates that the spine attaches directly to the node. A value greater than 0.0 (and less than 1.0) indicates that the spine attaches somewhere along the edge. The parent node is the node that is closer to the soma than the identified node. See also Saving the Model and Importing Models.

Example 1:Spine X has SWC-NODE-ID = 7 and SWC-NODE-OFFSET = 0.0

(SOMA)---------(6)---------(7)---------(8)--...
                            |
                            |
                           (X)


Example 2:Spine X has SWC-NODE-ID = 7 and SWC-NODE-OFFSET = 0.4

(SOMA)---------(6)---------(7)---------(8)--...
                       |
                       |
                      (X)

ATTACH-X, ATTACH-Y, ATTACH-Z: The exact x,y,z coordinate of the attachment point of the spine on the medial axis of the model.

SOMA-DISTANCE: The total dendritic length from the point of attachment of the spine to the closest model node marked as soma (or origin node if none marked).

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Send questions or comments to: alfredo.rodriguez@mssm.edu