User Guide

This guide provides practical how-to documentation for common PyFlowReg workflows and configurations.

Workflows

Learn how to use PyFlowReg in different processing scenarios:

• Array-Based Workflow - In-memory processing for smaller datasets

• File-Based Workflow - Efficient processing of large video files

• Real-Time Processing - Online motion correction with adaptive reference

• Multi-Session Processing - Aligning multiple recordings across sessions

Configuration

Detailed guides for configuring motion correction:

• OFOptions Reference - Complete parameter reference

• Quality Settings - Speed vs accuracy tradeoffs

• Preprocessing Options - Binning, filtering, normalization

• Reference Selection - Choosing reference frames

File Formats

Working with different file formats:

• Supported Formats - HDF5, TIFF, MAT, MDF

• Format Conversion - Converting between formats

• Multi-File Datasets - Handling multiple files

Parallelization

Optimizing performance with parallel processing:

• Choosing an Executor - Sequential, threading, multiprocessing

• Configuration - Tuning worker count and buffer size

• Performance Tips - Memory management and optimization