Rat hippocampus CA1

This Use Case places hippocampal neurons into a volume defined by an atlas. The Use Case can be found in Online Use Cases/Circuit Building/Cells placement/Hippocampus CA1.



The workflow is a sequence of independent steps manipulating volumetric data retrieved from the Neuroinformatics Platform. Each steps defines additional properties of the cells.

The sequence of steps is the following:

  • Define the region of interest based on the parcellation given by the atlas
  • Define cell positions based on given neuron densities
  • Define excitatory/inhibitory properties based on given ratio
  • Define ME-Type properties based on M-Type and E-Type ratio
  • Define the morphology to be used based on available morphologies and previously defined properties
  • Define cell orientation based on a computed orientation field in the volume

Input data:


Volume was adapted from Ropireddy et al., 2012

Cell composition

Morphoelectrical-type composition

We collected 146 electrophysiological single cell recordings from different neuron types (Alex Thomson, Audrey Mercer and colleagues) (Wistar rat - for the methods see Hughes et al., 2000; Pawelzik et al., 2002). We classified the recordings on the basis of stereotypical firing patterns (electrical types, e-types) according to the Petilla Convention (Ascoli et al., 2008) in response to depolarizing step current injections. For some e-types, we had too few recordings and for this reason we restricted the e-types to classical accommodating (cAC), bursting accommodating (bAC) and classical non-accommodating (cNAC). Each morphology type (m-type) can show multiple firing patterns, leading to different morpho-electrical types (me-types).

  cNAC cAC bAC
Ivy 33.33% 0.00% 66.67%
OLM 0.00% 100.00% 0.00%
PVBC 70.00% 0.00% 30.00%
CCKBC 0.00% 100.00% 0.00%
BS 75.00% 0.00% 25.00%
AA 0.00% 0.00% 100.00%
SCA 0.00% 100.00% 0.00%
PPA 0.00% 0.00% 100.00%
IS1 0.00% 100.00% 0.00%
IS3 0.00% 100.00% 0.00%
Tri 0.00% 100.00% 0.00%

Executing the Use Case

Execute the cell (SHIFT + ENTER) in the “Cell Placement Hippocampus Setup” notebook. Then navigate to the “Cell Placement Hippocampus” notebook and execute them sequentially (SHIFT + ENTER).

  1. positioning neurons

    This step computes cell positions with downscaled densities as an illustration. It then displays the cell positions in a widget.

  2. defining excitatory/inhibitory property

    This step computes the excitatory/inhibitory property based on the provided ratio and displays it in a widget.

  3. defining M-Type and E-Type properties

    This step computes the M-Type property and E-Type property at the same time and displays them in a widget.

    M-Type property:


    E-Type property:

  4. defining morphology for the cell position

    This step computes which morphology will be assigned to a particular cell position.

  5. defining cell orientation

    This steps computes the 3 vector fields X, Y, and Z and uses them to orient each neuron.

    X vector field:


    Y vector field:


    Z vector field: