Explanation

Conceptual material that builds understanding. These pages explain why things work the way they do, discuss tradeoffs and failure modes, and provide the theoretical background for PhenoTypic’s algorithms.

Core Concepts

• The Pipeline Mental Model
• Color Spaces for Phenotyping
• How the Image Class Works

Detection & Processing

• Detection Strategies Compared
• Grid vs Non-Grid Detection
• What Enhancement Actually Does
• Refinement Strategies

Measurement & Analysis

• Measurement Classification: Phenotypes vs. Features
• Measurement Metrics and Their Biological Meaning
• Metadata column namespace (REMBI modules)
• Edge Effects in Plate-Based Assays
• Image Quality: Noise, Contrast, and Structure
• The Linear-Softplus and Double-Softplus Growth Models

Specialized Topics

• The Filamentous Fungi Detection Algorithm
• Prefab Pipelines: Which One for Which Organism