###################
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*.

Approach:
---------

      .. image:: images/workflow.png
         :width: 373px
 

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**

Volume was adapted from `Ropireddy et al., 2012 <http://krasnow1.gmu.edu/cn3/hippocampus3d/>`_


**Cell composition**

- Total number of cells: 350000 `(adult rat - Bezaire and Soltesz, 2013) <https://doi.org/10.1002/hipo.22141>`_

- EI ratio: 89:11 `(adult rat - Bezaire and Soltesz, 2013) <https://doi.org/10.1002/hipo.22141>`_

- Percentage of neuron types from `(Bezaire and Soltesz, 2013 - adult rat) <https://doi.org/10.1002/hipo.22141>`_

 
**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 <http://www.sciencedirect.com/science/article/pii/S0165027000002545>`_; 
`Pawelzik et al., 2002 <http://onlinelibrary.wiley.com/doi/10.1002/cne.10118/abstract>`_). 
We classified the recordings on the basis of stereotypical firing patterns 
(electrical types, e-types) according to the Petilla Convention 
`(Ascoli et al., 2008) <https://www.ncbi.nlm.nih.gov/pubmed/18568015>`_ 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.

      .. image:: images/position.png
         :width: 600px

2. defining excitatory/inhibitory property

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

      .. image:: images/ei.png
         :width: 600px

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:
   
      .. image:: images/mtype.png
         :width: 600px

   E-Type property:
   
      .. image:: images/etype.png
         :width: 600px
4. defining morphology for the cell position
   
   This step computes which morphology will be assigned to a particular cell position.
   
      .. image:: images/morphology.png
         :width: 600px

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:

      .. image:: images/x.png
         :width: 600px
                 
   Y vector field:
   
      .. image:: images/y.png
         :width: 600px
                 
   Z vector field:

      .. image:: images/z.png
         :width: 600px