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 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)--...
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(X)
Example 2:Spine X has SWC-NODE-ID = 7 and SWC-NODE-OFFSET = 0.4
(SOMA)---------(6)---------(7)---------(8)--...
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(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).