Analysis_Zebrafish

A framework for analyzing the calcium imaging of zebrafish

Getting Started

git clone https://github.com/Knerlab/neural-activity-analysis.git
cd neural-activity-analysis
conda create --name zebrafish --file requirements.txt
conda activate zebrafish

Dataset: we release some of the datasets used in paper here.

Zebrafish Brain Atlas: can be download here

Demo Example

python demo.py

Data Preprocessing

python preprocess.py

Including the correction of motion artifacts, environmental lights artifacts, and signal normalizing

ROI segmentation and signal extraction

python ROIExtraction.py

need to set the path of the atlas

Dynamic Functional Connectivity Analysis

python meta_analysis_FC.py

Spectra Analysis

python meta_analysis_fre_ROI.py