Building required files

This documentation will cover how to build files required for the /data/ directory.

Building synapse weights

Synaptic weights from interneurons to grid cells are created with the generate_weights.m file. The included generate_weights.m file should be used to generate the synapse_weights.csv file for the project. The synapse_weights.csv file should be copied to the /data/ folder.

grc_to_in_conns.csv

The grc_to_in_conns.csv file includes connectivity data from grid cells to interneurons. It should be generated by setting the variable:
#define use_saved_g_to_i_conns 0 in general_params.cpp, and then running the simulation. Once the grc_to_in_conns.csv file is created, the variable can be set to:
#define use_saved_g_to_i_conns 1
This allows running the simulation to take less time by not needing to recompute it. This csv file is built by using the cent_x and cent_y variables to select where center-surround connections should be positioned based on grid cell to interneuron connections. The file plot_weights.m can be used to view the positioning of center-surround rings once generate_weights.m is run and a comb_syn_wts object is in Matlab memory from that script.

ext_dir_initial.cpp, ext_dir.cpp, init_firings.cpp

These files are included in the Github repo. They may need to be altered to fit the sizes of the grid cell layer used in the simulation.

ext_dir_initial.cpp

ext_dir_initial.cpp provides inital current levels from conjuntive cells to grid cells. The filename refers to external (to the grid cell layer) directional signal initial input. The script generate_ext_dir_initial.m can produce ext_dir_initial.cpp. The number of entries in the ext_dir_initial matrix should equal the grid cell layer size because the conjunctive cell to grid cell connections have one-to-one connectivity. ext_dir_initial_rot_l.cpp and ext_dir_initial_rot_r.cpp can potentially help initialize the grid pattern at a 90 or 0 degree rotation.

Scripts have been included that can help with the resizing of the vectors. Those scripts are resize_ext_dir.m and resize_ext_dir_init.m.

ext_dir.cpp

ext_dir.cpp stores values used in the vector of current levels from conjuntive cells to grid cells. Its size should match the total number of neurons in the grid cell layer.

init_firings.cpp

init_firings.cpp sets inital firing amounts in grid cells. The vector from init_firings.cpp might not need to be resized if the grid cell layer size is at least 30x30.

Animal data

The instructions in the “converting animal recordings” documentation should be followed if animal data is to be used in the simulation. This will supply the required data files in the /data/ directory.