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.. _network_file_content: | ||
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==================== | ||
Network File Content | ||
==================== | ||
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File Content Description | ||
------------------------ | ||
hdf5 is the file format used for storing the Network object. The network is stored in a layered format. The first layer consists of the network attributes. | ||
The attributes of the network are then broken down until the network can be representated as a collection of key value pairs. For example - cell_types is a network | ||
attribute therefore in the first layer. The description of each cell type is in layer 2. Each cell has various sections. The description of a section is in layer 3. | ||
Below are the attributes of the network. | ||
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object_type : str | ||
Type of object (Network) saved. | ||
N_pyr_x : int | ||
Nr of cells (x). | ||
N_pyr_y : int | ||
Nr of cells (y). | ||
threshold : float | ||
Firing threshold of all cells. | ||
celsius : float | ||
Temperature in degree celsius. | ||
cell_types : dict of Cell Object | ||
key : name of cell type. | ||
value : Cell object. | ||
gid_ranges : dict of dict | ||
key : cell name or drive name. | ||
value : dict. | ||
pos_dict : dict | ||
key : cell type name. | ||
value : All co-ordintes of the cell types. | ||
cell_response : Instance of Cell Response Object | ||
The Cell Response object. | ||
external_drives : dict of dict | ||
key : external drive name. | ||
value : dict. | ||
external_biases : dict of dict | ||
key : external bias name. | ||
value : dict. | ||
connectivity : list of dict | ||
Contains connection info between cells and | ||
cells and external drives. | ||
rec_arrays : dict of Extracellular Arrays | ||
key : extracellular array name. | ||
value : Instance of Extracellular Array object. | ||
delay : float | ||
Synaptic delay in ms. | ||
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Cell Type Description | ||
--------------------- | ||
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cell_name : str | ||
Name of the cell. | ||
pos : tuple | ||
The (x, y, z) coordinates. | ||
sections : dict of Section | ||
Dictionary with keys as section name. | ||
synapses : dict of dict | ||
Keys are name of synaptic mechanism. Each synaptic mechanism | ||
has keys for parameters of the mechanism, e.g., 'e', 'tau1', | ||
'tau2'. | ||
cell_tree : dict of list | ||
Stores the tree representation of a cell. | ||
sect_loc : dict of list | ||
Can have keys 'proximal' or 'distal' each containing | ||
names of section locations that are proximal or distal. | ||
gid : int | ||
GID of the cell in a network (or None if not yet assigned). | ||
dipole_pp : list of h.Dipole() | ||
The Dipole objects (see dipole.mod). | ||
vsec : dict | ||
Recording of section specific voltage. Must be enabled | ||
by running simulate_dipole(net, record_vsec=True) or | ||
simulate_dipole(net, record_vsoma=True). | ||
isec : dict | ||
Contains recording of section specific currents indexed | ||
by synapse type (keys can be soma_gabaa, soma_gabab etc.). | ||
Must be enabled by running simulate_dipole(net, record_isec=True) | ||
or simulate_dipole(net, record_isoma=True). | ||
tonic_biases : list of h.IClamp | ||
The current clamps inserted at each section of the cell | ||
for tonic biasing inputs. | ||
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Section Description | ||
------------------- | ||
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L : float | ||
length of a section in microns. | ||
diam : float | ||
diameter of a section in microns. | ||
cm : float | ||
membrane capacitance in micro-Farads. | ||
Ra : float | ||
axial resistivity in ohm-cm. | ||
end_pts : list of [x, y, z] | ||
The start and stop points of the section. | ||
syns : list of str | ||
The synaptic mechanisms to add in this section. | ||
mechs : dict | ||
Mechanisms to insert in this section. The keys | ||
are the names of the mechanisms and values | ||
are the properties. | ||
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Gid Range Description | ||
--------------------- | ||
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start : int | ||
Start of the gid_range. | ||
stop : int | ||
End of the gid_range. | ||
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External Drive Description | ||
-------------------------- | ||
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name : str | ||
Unique name for the drive. | ||
dynamics : dict | ||
Parameters describing how the temporal dynamics of spike trains in the | ||
drive. The keys are specific to the type of drive ('evoked', 'bursty', | ||
etc.). | ||
location : str | ||
Target location of synapses. | ||
cell_specific : bool | ||
Whether each artifical drive cell has 1-to-1 (True, default) or | ||
all-to-all (False) connection parameters. | ||
weights_ampa : dict or None | ||
Synaptic weights (in uS) of AMPA receptors on each targeted cell | ||
type (dict keys). | ||
weights_nmda : dict or None | ||
Synaptic weights (in uS) of NMDA receptors on each targeted cell | ||
type (dict keys). | ||
probability : dict or float | ||
Probability of connection between any src-target pair. | ||
synaptic_delays : dict or float | ||
Synaptic delay (in ms) at the column origin, dispersed laterally as | ||
a function of the space_constant. If float, applies to all target | ||
cell types. | ||
event_seed : int | ||
Optional initial seed for random number generator. | ||
conn_seed : int | ||
Optional initial seed for random number generator. | ||
n_drive_cells : int | 'n_cells' | ||
The number of drive cells that each contribute an independently | ||
sampled synaptic spike to the network according to the Gaussian | ||
time distribution (mu, sigma). | ||
events : list | ||
Contains the spike times of exogeneous inputs. | ||
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External Bias Description | ||
------------------------- | ||
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cell_type : str | ||
The cell type whose cells will get the tonic input. | ||
amplitude : float | ||
The amplitude of the input. | ||
t0 : float | ||
The start time of tonic input (in ms). | ||
tstop : float | ||
The end time of tonic input (in ms). | ||
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Connection Description | ||
---------------------- | ||
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target_types : str | ||
Cell type of target gids. | ||
target_gids : list of int | ||
Identifer for targets of source cells. | ||
num_targets : int | ||
Number of unique target gids. | ||
src_type : str | ||
Cell type of source gids. | ||
src_gids : list of int | ||
Identifier for source cells. | ||
num_srcs : int | ||
Number of unique source gids. | ||
gid_pairs : dict | ||
dict indexed by src gids. | ||
loc : str | ||
Target location of synapses. | ||
receptor : str | ||
Synaptic receptor of connection. | ||
nc_dict : dict | ||
Contains information about delay, weight, lamtha etc. | ||
allow_autapses : bool | ||
If True, allow connecting neuron to itself. | ||
probability : float | ||
Probability of connection between any src-target pair. | ||
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Extracellular Array Description | ||
------------------------------- | ||
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positions : tuple | list of tuple | ||
The (x, y, z) coordinates (in um) of the extracellular electrodes. | ||
conductivity : float | ||
Extracellular conductivity, in S/m. | ||
method : str | ||
Approximation to use. |
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