This a project for MRes in Neurotechnology 2018 - 2019 We investigate varies quantitative method to analysis data collected from mice LGN. Before running those code, make sure you modify the path in SetGlobalVars.m file first.

This project is devided into several stages:

1.Data Generation Extract usable data from raw data/spike sorted data located in farm(now farm2).

2.Data Clearning Eliminate subject/mice, cell, experiment which is correpted or have missing data.

3.Combining Combine data we have extracted and processed with data from silvia/jiaying. The combined or fixed new dataset is saved as "lgn_characterization_cells_ver_0.1.mat", under ROOT/data folder.

4.Receptive Field Extraction Major workload, extract receptive field via quadratic mutual infomation method. only one (linear) receptive field has been extracted. receptive field is assumed to depend on the 5 window step before, each window step lasts 50ms. The derived receptive field is a WxHxT tensor (or multi-dimensional array over real field)

5.Receptive field Gaussian fitting We first identify the existance of receptive field structure by look at the We then reparameterise by difference of gauss model. In essence, its difference of two gaussian in spatial and temporal domain. This distribution iof the amplitute in spatial domain and temporal domain are both gaussian. We assume there are two opposite component, which one is ON and the other is OFF. There are small group of cells can not be captured by this model, so we have defined a slightly more complexed model with two additional components to capture this.

6.Manually verify the fitting Plot all cells been generated and verify gaussian fitting is valid

7.Generate the Statistics from Gaussian Model parameters and DSI OSI etc Generate graphs

To run the demo of this project, try: main.m

root | |--data | |--subject_info | | |--m0679_mea1.mat This file contain all experimental infomation of subject m0679 measurement 1 | | ... | |-- CNM.mat contrst noise movie stimulus for receptive field analysis | |-- lgn_characteristic.mat NOTE!!!rf_stimtimes and rf_spiketimes are corrupted, do not use | ... |--src source code for varies analysis | |-- visualization | |-- pro_process | ... |--third_party third party libraries used |-- +qmi qudratic information receptive field analysis toolbox ...