Python Scripts and Results


This repository contains scripts that demonstrates presence of high-order cell assemblies from wide-field calcium imaging data. This is a collabo.pngrative project with Prof. Spencer Smith and Dr. Yiyi Yu from University of North Carolina, Chapel Hill. Part of the results has been presented at the 3rd International Conference on Mathematical Neuroscience. The conference submission and presentation can be found in icmns_submission

Data preprocessing

Run the script combine_datasets.m to pre-process the data. The data should be stored in the data/ directory. Each directory contains a different experiment. For each experiment, there are simultaneous recording from the primary visual cortex (V1, Combo3_V1.mat) and a higher visual cortex (area AL, Combo3_AL.mat).

These files can be opened via Matlab, or using the mat4py library.

Decrease sparsity over trials

Run the script to see the decreasing sparsity across repeated trials. You can change the area variable to see the result for V1 or AL. The summary plots will be saved in figures/sparsity/. Below is an example result for area AL.

In [1]:
%matplotlib inline

Number of cells: 352
Number of cells: 375
<matplotlib.figure.Figure at 0x105839a10>
Number of cells: 147
<matplotlib.figure.Figure at 0x11da17190>
Number of cells: 226
<matplotlib.figure.Figure at 0x10796fd50>
Number of cells: 375
<matplotlib.figure.Figure at 0x1057b6c50>
Number of cells: 590
<matplotlib.figure.Figure at 0x11d386290>
Number of cells: 189
<matplotlib.figure.Figure at 0x10579d290>
<matplotlib.figure.Figure at 0x107981b50>

Presence of high-order cell assemblies

Run the script analyze_data_populaiton.m to see evidence of high-order cell assemblies. The script will generate the following result for each experiment session

  • sparsity over trial (figures/sparseness_over_timestim*, Fig. 1C)
  • subset index calculation (figures/subset_indexstim* Fig. 1D)
  • Number of unique high-order cell assemblies (cellAssembly_* Fig. 1E)
  • Accuracy of cell assembly occurance time (cellAssemblyjitter*, Fig. 1F)
  • Example raster plots (figures/exampleRasterStim* slide #27)

In [ ]: