Routine Name:
volumeconnect
Description:
Establishes synaptic connections between groups of
elements
based on the x-y-z positions of the elements. This routine
sets up the connections by adding SPIKE messages between the
source and destination objects.
Usage:
volumeconnect source_elements destination_elements \
-relative \
-sourcemask {box, ellipsoid} x1 y1 z1 x2 y2 z2 \
-sourcehole {box, ellipsoid} x1 y1 z1 x2 y2 z2 \
-destmask
{box, ellipsoid} x1 y1 z1 x2 y2 z2 \
-desthole
{box, ellipsoid} x1 y1 z1 x2 y2 z2 \
-probability p
source_elements A wildcarded list of elements which are the
sources of the SPIKE messages. These must be of
class "spiking" and are usually spikegen or
randomspike objects.
destination_elements A wildcarded list of elements which are
the destinations of the SPIKE messages. These must
be synchans or objects derived from synchan.
-relative This option means that connections will be set up
based on the locations of destination objects
relative to source objects. If this option is not
selected, the absolute locations of source and
destination elements will be used to determine
which connections are to be set up.
-sourcemask {box, ellipsoid} x1 y1 z1 x2 y2 z2 -- This
specifies a rectangular or ellipsoidal region from
which source elements are to be taken. If the "box"
option is used, then x1, y1, and z1 are the minimum
x, y, and z values of the region while x2, y2, and
z2 are the maximum x, y, and z values of the
region. If the "ellipsoid" option is used, then the
source region is an ellipsoid with x1, y1 and z1
representing the center of the ellipsoid while x2,
y2, and z2 represent the lengths of the principal
axes in the x, y, and z directions respectively.
Note that to choose a spherical region x2, y2, and
z2 must be equal. Note also that one or the other
of {box, ellipsoid} MUST be chosen; leaving both of
them out will generate an error. Finally, one can
choose multiple source regions by having multiple
-sourcemask options. The same conventions are
followed for the next three options.
-sourcehole {box, ellipsoid} x1 y1 z1 x2 y2 z2 -- This
specifies a rectangular or elliptical region NOT to
include in the source region(s). You can exclude
multiple regions by having multiple -sourcehole
options.
-destmask {box, ellipsoid} x1 y1 z1 x2 y2 z2 -- This
specifies a rectangular or elliptical region to which
SPIKE messages will be sent.
-desthole {box, ellipsoid} x1 y1 z1 x2 y2 z2 -- This
specifies a rectangular or elliptical region NOT to
include in the destination region(s).
-probability p -- This option causes connections to be
made with a probability p, which must be in the
range [0,1]. This allows probabilistically-connected
networks to be set up.
Example:
Say we want to connect the spike generating-region of a group
of cells with excitatory synapses on the apical dendritic
compartments of the same group of cells, without connecting
any cell to itself. We could do this:
volumeconnect /cell[]/soma/spike
/cell[]/apical_dend/exc_syn
-relative
-sourcemask box -1 -1 -1 1 1 1
-sourcehole box -10e-6 -10e-6 -1
10e-6 10e-6 1
\
-destmask
box -1 -1 -1 1 1 1
\
\
\
\
\
Note that here we are excluding a region 10 microns square
in
the x and y direction (but essentially unlimited in the z
direction) so that cells don't connect to themselves. Here
I'm assuming we're using SI units. This could also have
been done with planarconnect. Note also that the usual way
to specify "all cells in a region" is to give source or
destination regions using -sourcemask or -destmask with
limits far greater than the entire extent of all the
elements in the region.
Notes:
except
This routine is almost identical with planarconnect
that it uses the positions of elements in three dimensions
to specify whether connections are made or not, whereas
planarconnect uses only the x and y dimensions.
The weights and delays of the connections set up by this
command are typically specified using the volumeweight and
volumedelay commands, although they can be set up by hand.
See also:
on
planarconnect, volumeweight, volumedelay; Chapter 18
of the Book of GENESIS (2nd ed.) has a lengthy discussion
this and related commands.