User Guide

This section covers each step in the pipeline, parameters and metadata in more detail.

Usage

• 1. Assembly
  • 1.1. Overview
  • 1.2. Inputs
  • 1.3. Outputs
  • 1.4. Validate Outputs
• 2. Registration
  • 2.1. Overview
  • 2.2. Inputs
  • 2.3. Rigid Registration
  • 2.4. Non-rigid Registration
  • 2.5. Outputs
  • 2.6. Validate Outputs
• 3. Segmentation
  • 3.1. Segmentation Overview
  • 3.2. Inputs
  • 3.3. Tuning CNMF
  • 3.4. Segmentation Outputs
• 4. Axial Collation and Correction
  • 4.1. Inputs
  • 4.2. Outputs
• 5. Tips and Tricks
  • 5.1. Exploring Datasets in MATLAB
  • 5.2. Fullfile
  • 5.3. Learn about Functions
  • 5.4. Parallel Processing
  • 5.5. Find MATLAB Install Location
• 6. Troubleshooting
  • 6.1. Memory
  • 6.2. Missing Compiled Binary (Windows)
  • 6.3. Matlab Server Issues
  • 6.4. Windows Filepaths