# Prefab Pipelines: Which One for Which Organism

Prefab pipelines are pre-configured `ImagePipeline` subclasses that
bundle operations, refiners, and measurements into a single ready-to-use
workflow. Each is tuned for a specific imaging scenario.

## Overview

| Prefab | Organism | Plate type | Key strategy |
|--------|----------|-----------|--------------|
| `HeavyOtsuPipeline` | Yeast, bacteria | 96/384-well grid | Multi-stage Otsu with refinement |
| `HeavyWatershedPipeline` | Yeast, bacteria | Dense grids | Watershed for touching colonies |
| `RoundPeaksPipeline` | Yeast | Grid plates | Peak detection, lightweight |
| `HeavyRoundPeaksPipeline` | Yeast | Grid plates | Extended peak detection with refinement |
| `FilamentousFungiPipeline` | *Neurospora*, *Aspergillus*, etc. | Grid plates | BM3D + FilamentousFungiDetector |
| `GridSectionPipeline` | Any | Pre-tiled sections | Per-section processing |

## HeavyOtsuPipeline

**Best for:** General-purpose colony detection on clean, well-lit plates
with uniform backgrounds.

**Pipeline steps:**
GaussianBlur → CLAHE → MedianFilter → SobelFilter → OtsuDetector →
MaskOpener → BorderObjectRemover → SmallObjectRemover → MaskFill →
GridOversizedObjectRemover → ReduceMultipleGridObjects → GridAligner

**Measurements:** MeasureShape, MeasureColor, MeasureTexture,
MeasureIntensity

**When to choose:** This is the default starting point. Try it first;
switch to a specialized prefab only if results are unsatisfactory.

## HeavyWatershedPipeline

**Best for:** Plates where colonies grow large enough to touch or
overlap. Watershed segmentation separates merged colonies that Otsu
would detect as a single object.

**When to choose:** Colony overlap is visible in the overlay — adjacent
colonies sharing a boundary without clear separation.

## RoundPeaksPipeline

**Best for:** Grid plates with well-separated round colonies. Faster
than the Heavy pipelines because it uses fewer refinement steps.

**When to choose:** Speed matters and colonies are round, well-spaced,
and clearly visible.

## FilamentousFungiPipeline

**Best for:** Filamentous organisms with branching hyphae. Uses BM3D
denoising, homomorphic illumination correction, and the specialized
`FilamentousFungiDetector` with Dijkstra reconnection.

**When to choose:** The organism grows as a mycelial network rather
than a compact round colony. Standard detectors miss the outer hyphae.

## Customizing Prefabs

Prefabs expose their key parameters through `__init__`:

```python
from phenotypic.prefab import HeavyOtsuPipeline

pipeline = HeavyOtsuPipeline(
    gaussian_sigma=3,       # Stronger blur
    small_object_min_size=100,  # Remove larger fragments
    benchmark=True,         # Track execution times
)
```

For more extensive customization, build a pipeline from scratch using
`ImagePipeline(ops=[...], meas=[...])`.