Neuron's connection on Shape plot
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Neuron's connection on Shape plot
How can i show connections between neurons in the shape plot?
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ted
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Re: Neuron's connection on Shape plot
This will be a do-it-yourself project. First, you need an instance of the Shape class that renders your cells in the appropriate locations*, and with the desired orientations**. Then you can use the Shape class's beginline and line (and maybe also mark, to put a dot at the synaptic location) to draw the connections from presynaptic cell to the location of the synapse on the target cell***. You'll find documentation of the Shape class in the Programmer's Reference.
* and **--assuming that your cell morphologies are based on detailed morphometric data:
Location of the entire cell is controlled by the xyz coordinates of the pt3d data that define the root section. To move an entire cell to a new location it is only necessary to apply a translation operation to those coordinates.
Orientation is controlled by the sequence of xyz coordinates along each section. To change the orientation of a cell it is necessary to apply a rotation operation to the xyz coordinates of all pt3d data throughout the entire cell.
***--An example of how to find the xyz coordinates of the origin and terminus of a line that connects a presynaptic cell to a target synapse:
For the sake of this example, assume that the NetCon that connects the spike source to the target synapse monitors cell[1].axon.v(0.5), and that it delivers events to a synaptic mechanism attached to cell[2].dend(0.3).
The x3d, y3d, z3d data that belong to cell[1].axon define a path in space. Find the point along this path that is midway between its 0 and 1 ends. This is the origin of the line you will want to draw.
The x3d, y3d, z3d data that belong to cell[2].dend define another path in space. Find the point along this path that is 30% of the distance from its 0 end. This is the terminus of the line you will want to draw.
* and **--assuming that your cell morphologies are based on detailed morphometric data:
Location of the entire cell is controlled by the xyz coordinates of the pt3d data that define the root section. To move an entire cell to a new location it is only necessary to apply a translation operation to those coordinates.
Orientation is controlled by the sequence of xyz coordinates along each section. To change the orientation of a cell it is necessary to apply a rotation operation to the xyz coordinates of all pt3d data throughout the entire cell.
***--An example of how to find the xyz coordinates of the origin and terminus of a line that connects a presynaptic cell to a target synapse:
For the sake of this example, assume that the NetCon that connects the spike source to the target synapse monitors cell[1].axon.v(0.5), and that it delivers events to a synaptic mechanism attached to cell[2].dend(0.3).
The x3d, y3d, z3d data that belong to cell[1].axon define a path in space. Find the point along this path that is midway between its 0 and 1 ends. This is the origin of the line you will want to draw.
The x3d, y3d, z3d data that belong to cell[2].dend define another path in space. Find the point along this path that is 30% of the distance from its 0 end. This is the terminus of the line you will want to draw.