Cell groups#

Cell groups represent a union of cells of a single kind simulated in lockstep. In a sense, their existence is an optimisation, since parts of the internal state and computations can be shared between cell in single group. The currently most complicated cell group is the one for cable cells, called cable_cell_group (mc stands for multi-compartment, used in older parts of Arbor), so we will focus on this type here.

Cell groups are created by domain decomposition methods on consideration of soft (like performance optimisation) and hard (cells connected by gap junctions must be in the same group) constraints.

Cable Cell group cable_cell_group#

Cable cell groups have backing store in shared_state (given the introduction, we now understand that the shared stands for ‘shared’ between cell in a group). In this data set, we also collect the private data of mechanisms. One thing to watch out for here is that instances of the same mechanism on a cell group will be collated.

Let us examine an example of such a cell group; assume the following

  1. the group comprises two cells with a total of 9 CVs 1. cell 0 has 4 CVs 2. cell 1 has 5 CVs

  2. pas has been painted on three regions and collated 1. region 0 covers CVs [0 1 2] 2. region 1 covers CV 5 3. region 2 covers CV 7

  3. pas has two parameters g (conductance density) and E (resting potential)

- shared_state
  - mechanisms
    - id 0
      - name   "pas"
      - width  5
      - parameters
        - id 0
          - name "g"
          - values [* * * * *]
        - id 1
          - name "E"
          - values [* * * * *]
      - index  [0 1 2 5 7]
                / | | |  \
               / / /  |  |
              / / /    \  \
  - voltage [* * * * * * * * *]

Mechanisms access their view of the cell group data via the arb_mechanism_ppack structure. To continue with our example, the pas mechanism would iterate through its view on the cell group voltage to compute the current density i like this

for ix in 0..width
  # Obtain parameters
  g  = ppack.parameters["g"][ix]
  E  = ppack.parameters["E"][ix]
  # Fetch voltage, note the indirection
  cv = ppack.index[ix]
  u  = ppack.voltage[cv]
  # Write outgoing current
  ppack.i[ix] = g*(u - E)

In general, cell group wide quantities (like voltage here) need to be indexed via ppack.index. Note, that the layout of parameters in ppack is this in reality:

- ppack
  - parameters   [g g g g g E E E E E]

When using NMODL, we translate names like g to offsets into the parameter array at compile time. Handwritten mechanisms need to do this manually.