Dual-Color Image Processing Pipeline

This repository contains a dual-color image processing pipeline implemented in Matlab. The pipeline accomplishes the extraction and correction of whole-brain calcium activity in freely swimming zebrafish by processing data acquired by a two-color light field imaging system. Please check our paper "All-optical interrogation of brain-wide activity in freely swimming larval zebrafish" for more details.

Pipeline

The pipeline consists of the following main steps:

• Dual-color 3D Image Reconstruction
• Image Registration
• Region Segmentation and Signal Extraction
• Adaptive Filter Calcium Signal Correction