User Guide

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

• 1. Image Assembly
  • 1.1. Overview
  • 1.2. scanreader
  • 1.3. Save your data
  • 1.4. Data Preview
  • 1.5. Command Line Usage
  • 1.6. Assembly Benchmarks
• 2. Batch Utils
  • 2.1. Overview
  • 2.2. Create a Batch
  • 2.3. Add a batch item
  • 2.4. Run a batch item
  • 2.5. Command Line Usage Overview:
  • 2.6. Examples
• 3. Registration
  • 3.1. Overview
  • 3.2. Registration Parameters
  • 3.3. Registration Results
  • 3.4. Summary and Metrics
  • 3.5. Summary and Metrics
• 4. Segmentation
  • 4.1. CNMF Parameters
• 5. Z-Plane Collation