Neural Activity Analysis Pipeline for Multi-Electrode Array (MEA) Data (Collaboration with Bang Lab)
Analysis pipeline for processing and analyzing neural activity from Multi-Electrode Array recordings, with a focus on spike train analysis, oscillatory burst detection, and spectral parameterization.
Raw MEA Data (.spk)
↓ MATLAB
Individual Well Files (.mat)
↓ MATLAB
Combined Plate Structure (.mat)
↓ Python
Spike Train Processing (JSON)
↓ Python
Spectral Analysis (Pickle)
↓ Python
Burst Analysis & Results (CSV)
-
AxionFileLoader Toolbox
- Add to MATLAB path
-
natsortfiles Function
- Download from MATLAB File Exchange
- Used for natural sorting of filenames
Install dependencies using pip, or create the environment from .yml:
conda create --name environment_NDD.ymlyour_project/
├── matlab/
│ ├── mea_data_conversion_script.m
│ └── MEA_convert_spk.m
├── python/
│ ├── plate_processor.py
│ ├── spectral_analyzer.py
│ └── oscillatory_burst_analyzer.py
├── environment_NDD.yml
├── README.md
└── data/
├── raw_recordings/ # .spk files
├── processed_plates/ # .mat files
├── spike_data/ # JSON files
├── spectral_analysis/ # Pickle files
└── burst_analysis/ # CSV results
In progress