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PhenoTypic PhenoTypic
  • Installation
  • Tutorials
  • How-To Guides
  • Explanation
  • Extending PhenoTypic
    • API Reference
    • Developer Guide
    • Downloads
  • GitHub
  • Installation
  • Tutorials
  • How-To Guides
  • Explanation
  • Extending PhenoTypic
  • API Reference
  • Developer Guide
  • Downloads
  • GitHub

Section Navigation

Correction & Preprocessing

  • How To: Correct Grid Rotation
  • How To: Enhance Low-Contrast Images
  • How To: Crop and Pad Images for Batch Consistency
  • How To: Denoise Low-Light Images

Detection & Refinement

  • How To: Choose a Detection Algorithm
  • How To: Refine Noisy Detection Boundaries
  • How To: Manual Grid Detection When Automatic Fails
  • How To: Combine Detectors with CompositeDetector
  • How To: Merge Fragmented Detections
  • GPU-Accelerated Colony Detection

Measurement & Analysis

  • How To: Measure Colony Size and Intensity
  • How To: Correct Edge Effects in Plate Assays
  • How To: Fit Logistic Growth Models
  • How To: Assess Image Quality Before Pipeline Design

CLI & Infrastructure

  • CLI Batch Processing
  • SLURM Pipelines
  • Parameter Sweeps
  • Serialize and Share Pipelines
  • Store Results in HDF5
  • Generate HTML Processing Reports
  • How-To Guides

How-To Guides#

Task-oriented recipes that solve a specific problem. Each guide is standalone – you can jump directly to the one you need.

Correction & Preprocessing

  • How To: Correct Grid Rotation
  • How To: Enhance Low-Contrast Images
  • How To: Crop and Pad Images for Batch Consistency
  • How To: Denoise Low-Light Images

Detection & Refinement

  • How To: Choose a Detection Algorithm
  • How To: Refine Noisy Detection Boundaries
  • How To: Manual Grid Detection When Automatic Fails
  • How To: Combine Detectors with CompositeDetector
  • How To: Merge Fragmented Detections
  • GPU-Accelerated Colony Detection

Measurement & Analysis

  • How To: Measure Colony Size and Intensity
  • How To: Correct Edge Effects in Plate Assays
  • How To: Fit Logistic Growth Models
  • How To: Assess Image Quality Before Pipeline Design

CLI & Infrastructure

  • CLI Batch Processing
  • SLURM Pipelines
  • Parameter Sweeps
  • Serialize and Share Pipelines
  • Store Results in HDF5
  • Generate HTML Processing Reports

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