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skills/histolab/SKILL.md

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+---
+name: histolab
+description: Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.
+---
+
+# Histolab
+
+## Overview
+
+Histolab is a Python library for processing whole slide images (WSI) in digital pathology. It automates tissue detection, extracts informative tiles from gigapixel images, and prepares datasets for deep learning pipelines. The library handles multiple WSI formats, implements sophisticated tissue segmentation, and provides flexible tile extraction strategies.
+
+## Installation
+
+```bash
+uv pip install histolab
+```
+
+## Quick Start
+
+Basic workflow for extracting tiles from a whole slide image:
+
+```python
+from histolab.slide import Slide
+from histolab.tiler import RandomTiler
+
+# Load slide
+slide = Slide("slide.svs", processed_path="output/")
+
+# Configure tiler
+tiler = RandomTiler(
+    tile_size=(512, 512),
+    n_tiles=100,
+    level=0,
+    seed=42
+)
+
+# Preview tile locations
+tiler.locate_tiles(slide, n_tiles=20)
+
+# Extract tiles
+tiler.extract(slide)
+```
+
+## Core Capabilities
+
+### 1. Slide Management
+
+Load, inspect, and work with whole slide images in various formats.
+
+**Common operations:**
+- Loading WSI files (SVS, TIFF, NDPI, etc.)
+- Accessing slide metadata (dimensions, magnification, properties)
+- Generating thumbnails for visualization
+- Working with pyramidal image structures
+- Extracting regions at specific coordinates
+
+**Key classes:** `Slide`
+
+**Reference:** `references/slide_management.md` contains comprehensive documentation on:
+- Slide initialization and configuration
+- Built-in sample datasets (prostate, ovarian, breast, heart, kidney tissues)
+- Accessing slide properties and metadata
+- Thumbnail generation and visualization
+- Working with pyramid levels
+- Multi-slide processing workflows
+
+**Example workflow:**
+```python
+from histolab.slide import Slide
+from histolab.data import prostate_tissue
+
+# Load sample data
+prostate_svs, prostate_path = prostate_tissue()
+
+# Initialize slide
+slide = Slide(prostate_path, processed_path="output/")
+
+# Inspect properties
+print(f"Dimensions: {slide.dimensions}")
+print(f"Levels: {slide.levels}")
+print(f"Magnification: {slide.properties.get('openslide.objective-power')}")
+
+# Save thumbnail
+slide.save_thumbnail()
+```
+
+### 2. Tissue Detection and Masks
+
+Automatically identify tissue regions and filter background/artifacts.
+
+**Common operations:**
+- Creating binary tissue masks
+- Detecting largest tissue region
+- Excluding background and artifacts
+- Custom tissue segmentation
+- Removing pen annotations
+
+**Key classes:** `TissueMask`, `BiggestTissueBoxMask`, `BinaryMask`
+
+**Reference:** `references/tissue_masks.md` contains comprehensive documentation on:
+- TissueMask: Segments all tissue regions using automated filters
+- BiggestTissueBoxMask: Returns bounding box of largest tissue region (default)
+- BinaryMask: Base class for custom mask implementations
+- Visualizing masks with `locate_mask()`
+- Creating custom rectangular and annotation-exclusion masks
+- Mask integration with tile extraction
+- Best practices and troubleshooting
+
+**Example workflow:**
+```python
+from histolab.masks import TissueMask, BiggestTissueBoxMask
+
+# Create tissue mask for all tissue regions
+tissue_mask = TissueMask()
+
+# Visualize mask on slide
+slide.locate_mask(tissue_mask)
+
+# Get mask array
+mask_array = tissue_mask(slide)
+
+# Use largest tissue region (default for most extractors)
+biggest_mask = BiggestTissueBoxMask()
+```
+
+**When to use each mask:**
+- `TissueMask`: Multiple tissue sections, comprehensive analysis
+- `BiggestTissueBoxMask`: Single main tissue section, exclude artifacts (default)
+- Custom `BinaryMask`: Specific ROI, exclude annotations, custom segmentation
+
+### 3. Tile Extraction
+
+Extract smaller regions from large WSI using different strategies.
+
+**Three extraction strategies:**
+
+**RandomTiler:** Extract fixed number of randomly positioned tiles
+- Best for: Sampling diverse regions, exploratory analysis, training data
+- Key parameters: `n_tiles`, `seed` for reproducibility
+
+**GridTiler:** Systematically extract tiles across tissue in grid pattern
+- Best for: Complete coverage, spatial analysis, reconstruction
+- Key parameters: `pixel_overlap` for sliding windows
+
+**ScoreTiler:** Extract top-ranked tiles based on scoring functions
+- Best for: Most informative regions, quality-driven selection
+- Key parameters: `scorer` (NucleiScorer, CellularityScorer, custom)
+
+**Common parameters:**
+- `tile_size`: Tile dimensions (e.g., (512, 512))
+- `level`: Pyramid level for extraction (0 = highest resolution)
+- `check_tissue`: Filter tiles by tissue content
+- `tissue_percent`: Minimum tissue coverage (default 80%)
+- `extraction_mask`: Mask defining extraction region
+
+**Reference:** `references/tile_extraction.md` contains comprehensive documentation on:
+- Detailed explanation of each tiler strategy
+- Available scorers (NucleiScorer, CellularityScorer, custom)
+- Tile preview with `locate_tiles()`
+- Extraction workflows and reporting
+- Advanced patterns (multi-level, hierarchical extraction)
+- Performance optimization and troubleshooting
+
+**Example workflows:**
+
+```python
+from histolab.tiler import RandomTiler, GridTiler, ScoreTiler
+from histolab.scorer import NucleiScorer
+
+# Random sampling (fast, diverse)
+random_tiler = RandomTiler(
+    tile_size=(512, 512),
+    n_tiles=100,
+    level=0,
+    seed=42,
+    check_tissue=True,
+    tissue_percent=80.0
+)
+random_tiler.extract(slide)
+
+# Grid coverage (comprehensive)
+grid_tiler = GridTiler(
+    tile_size=(512, 512),
+    level=0,
+    pixel_overlap=0,
+    check_tissue=True
+)
+grid_tiler.extract(slide)
+
+# Score-based selection (most informative)
+score_tiler = ScoreTiler(
+    tile_size=(512, 512),
+    n_tiles=50,
+    scorer=NucleiScorer(),
+    level=0
+)
+score_tiler.extract(slide, report_path="tiles_report.csv")
+```
+
+**Always preview before extracting:**
+```python
+# Preview tile locations on thumbnail
+tiler.locate_tiles(slide, n_tiles=20)
+```
+
+### 4. Filters and Preprocessing
+
+Apply image processing filters for tissue detection, quality control, and preprocessing.
+
+**Filter categories:**
+
+**Image Filters:** Color space conversions, thresholding, contrast enhancement
+- `RgbToGrayscale`, `RgbToHsv`, `RgbToHed`
+- `OtsuThreshold`, `AdaptiveThreshold`
+- `StretchContrast`, `HistogramEqualization`
+
+**Morphological Filters:** Structural operations on binary images
+- `BinaryDilation`, `BinaryErosion`
+- `BinaryOpening`, `BinaryClosing`
+- `RemoveSmallObjects`, `RemoveSmallHoles`
+
+**Composition:** Chain multiple filters together
+- `Compose`: Create filter pipelines
+
+**Reference:** `references/filters_preprocessing.md` contains comprehensive documentation on:
+- Detailed explanation of each filter type
+- Filter composition and chaining
+- Common preprocessing pipelines (tissue detection, pen removal, nuclei enhancement)
+- Applying filters to tiles
+- Custom mask filters
+- Quality control filters (blur detection, tissue coverage)
+- Best practices and troubleshooting
+
+**Example workflows:**
+
+```python
+from histolab.filters.compositions import Compose
+from histolab.filters.image_filters import RgbToGrayscale, OtsuThreshold
+from histolab.filters.morphological_filters import (
+    BinaryDilation, RemoveSmallHoles, RemoveSmallObjects
+)
+
+# Standard tissue detection pipeline
+tissue_detection = Compose([
+    RgbToGrayscale(),
+    OtsuThreshold(),
+    BinaryDilation(disk_size=5),
+    RemoveSmallHoles(area_threshold=1000),
+    RemoveSmallObjects(area_threshold=500)
+])
+
+# Use with custom mask
+from histolab.masks import TissueMask
+custom_mask = TissueMask(filters=tissue_detection)
+
+# Apply filters to tile
+from histolab.tile import Tile
+filtered_tile = tile.apply_filters(tissue_detection)
+```
+
+### 5. Visualization
+
+Visualize slides, masks, tile locations, and extraction quality.
+
+**Common visualization tasks:**
+- Displaying slide thumbnails
+- Visualizing tissue masks
+- Previewing tile locations
+- Assessing tile quality
+- Creating reports and figures
+
+**Reference:** `references/visualization.md` contains comprehensive documentation on:
+- Slide thumbnail display and saving
+- Mask visualization with `locate_mask()`
+- Tile location preview with `locate_tiles()`
+- Displaying extracted tiles and mosaics
+- Quality assessment (score distributions, top vs bottom tiles)
+- Multi-slide visualization
+- Filter effect visualization
+- Exporting high-resolution figures and PDF reports
+- Interactive visualization in Jupyter notebooks
+
+**Example workflows:**
+
+```python
+import matplotlib.pyplot as plt
+from histolab.masks import TissueMask
+
+# Display slide thumbnail
+plt.figure(figsize=(10, 10))
+plt.imshow(slide.thumbnail)
+plt.title(f"Slide: {slide.name}")
+plt.axis('off')
+plt.show()
+
+# Visualize tissue mask
+tissue_mask = TissueMask()
+slide.locate_mask(tissue_mask)
+
+# Preview tile locations
+tiler = RandomTiler(tile_size=(512, 512), n_tiles=50)
+tiler.locate_tiles(slide, n_tiles=20)
+
+# Display extracted tiles in grid
+from pathlib import Path
+from PIL import Image
+
+tile_paths = list(Path("output/tiles/").glob("*.png"))[:16]
+fig, axes = plt.subplots(4, 4, figsize=(12, 12))
+axes = axes.ravel()
+
+for idx, tile_path in enumerate(tile_paths):
+    tile_img = Image.open(tile_path)
+    axes[idx].imshow(tile_img)
+    axes[idx].set_title(tile_path.stem, fontsize=8)
+    axes[idx].axis('off')
+
+plt.tight_layout()
+plt.show()
+```
+
+## Typical Workflows
+
+### Workflow 1: Exploratory Tile Extraction
+
+Quick sampling of diverse tissue regions for initial analysis.
+
+```python
+from histolab.slide import Slide
+from histolab.tiler import RandomTiler
+import logging
+
+# Enable logging for progress tracking
+logging.basicConfig(level=logging.INFO)
+
+# Load slide
+slide = Slide("slide.svs", processed_path="output/random_tiles/")
+
+# Inspect slide
+print(f"Dimensions: {slide.dimensions}")
+print(f"Levels: {slide.levels}")
+slide.save_thumbnail()
+
+# Configure random tiler
+random_tiler = RandomTiler(
+    tile_size=(512, 512),
+    n_tiles=100,
+    level=0,
+    seed=42,
+    check_tissue=True,
+    tissue_percent=80.0
+)
+
+# Preview locations
+random_tiler.locate_tiles(slide, n_tiles=20)
+
+# Extract tiles
+random_tiler.extract(slide)
+```
+
+### Workflow 2: Comprehensive Grid Extraction
+
+Complete tissue coverage for whole-slide analysis.
+
+```python
+from histolab.slide import Slide
+from histolab.tiler import GridTiler
+from histolab.masks import TissueMask
+
+# Load slide
+slide = Slide("slide.svs", processed_path="output/grid_tiles/")
+
+# Use TissueMask for all tissue sections
+tissue_mask = TissueMask()
+slide.locate_mask(tissue_mask)
+
+# Configure grid tiler
+grid_tiler = GridTiler(
+    tile_size=(512, 512),
+    level=1,  # Use level 1 for faster extraction
+    pixel_overlap=0,
+    check_tissue=True,
+    tissue_percent=70.0
+)
+
+# Preview grid
+grid_tiler.locate_tiles(slide)
+
+# Extract all tiles
+grid_tiler.extract(slide, extraction_mask=tissue_mask)
+```
+
+### Workflow 3: Quality-Driven Tile Selection
+
+Extract most informative tiles based on nuclei density.
+
+```python
+from histolab.slide import Slide
+from histolab.tiler import ScoreTiler
+from histolab.scorer import NucleiScorer
+import pandas as pd
+import matplotlib.pyplot as plt
+
+# Load slide
+slide = Slide("slide.svs", processed_path="output/scored_tiles/")
+
+# Configure score tiler
+score_tiler = ScoreTiler(
+    tile_size=(512, 512),
+    n_tiles=50,
+    level=0,
+    scorer=NucleiScorer(),
+    check_tissue=True
+)
+
+# Preview top tiles
+score_tiler.locate_tiles(slide, n_tiles=15)
+
+# Extract with report
+score_tiler.extract(slide, report_path="tiles_report.csv")
+
+# Analyze scores
+report_df = pd.read_csv("tiles_report.csv")
+plt.hist(report_df['score'], bins=20, edgecolor='black')
+plt.xlabel('Tile Score')
+plt.ylabel('Frequency')
+plt.title('Distribution of Tile Scores')
+plt.show()
+```
+
+### Workflow 4: Multi-Slide Processing Pipeline
+
+Process entire slide collection with consistent parameters.
+
+```python
+from pathlib import Path
+from histolab.slide import Slide
+from histolab.tiler import RandomTiler
+import logging
+
+logging.basicConfig(level=logging.INFO)
+
+# Configure tiler once
+tiler = RandomTiler(
+    tile_size=(512, 512),
+    n_tiles=50,
+    level=0,
+    seed=42,
+    check_tissue=True
+)
+
+# Process all slides
+slide_dir = Path("slides/")
+output_base = Path("output/")
+
+for slide_path in slide_dir.glob("*.svs"):
+    print(f"\nProcessing: {slide_path.name}")
+
+    # Create slide-specific output directory
+    output_dir = output_base / slide_path.stem
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    # Load and process slide
+    slide = Slide(slide_path, processed_path=output_dir)
+
+    # Save thumbnail for review
+    slide.save_thumbnail()
+
+    # Extract tiles
+    tiler.extract(slide)
+
+    print(f"Completed: {slide_path.name}")
+```
+
+### Workflow 5: Custom Tissue Detection and Filtering
+
+Handle slides with artifacts, annotations, or unusual staining.
+
+```python
+from histolab.slide import Slide
+from histolab.masks import TissueMask
+from histolab.tiler import RandomTiler
+from histolab.filters.compositions import Compose
+from histolab.filters.image_filters import RgbToGrayscale, OtsuThreshold
+from histolab.filters.morphological_filters import (
+    BinaryDilation, RemoveSmallObjects, RemoveSmallHoles
+)
+
+# Define custom filter pipeline for aggressive artifact removal
+aggressive_filters = Compose([
+    RgbToGrayscale(),
+    OtsuThreshold(),
+    BinaryDilation(disk_size=10),
+    RemoveSmallHoles(area_threshold=5000),
+    RemoveSmallObjects(area_threshold=3000)  # Remove larger artifacts
+])
+
+# Create custom mask
+custom_mask = TissueMask(filters=aggressive_filters)
+
+# Load slide and visualize mask
+slide = Slide("slide.svs", processed_path="output/")
+slide.locate_mask(custom_mask)
+
+# Extract with custom mask
+tiler = RandomTiler(tile_size=(512, 512), n_tiles=100)
+tiler.extract(slide, extraction_mask=custom_mask)
+```
+
+## Best Practices
+
+### Slide Loading and Inspection
+1. Always inspect slide properties before processing
+2. Save thumbnails for quick visual review
+3. Check pyramid levels and dimensions
+4. Verify tissue is present using thumbnails
+
+### Tissue Detection
+1. Preview masks with `locate_mask()` before extraction
+2. Use `TissueMask` for multiple sections, `BiggestTissueBoxMask` for single sections
+3. Customize filters for specific stains (H&E vs IHC)
+4. Handle pen annotations with custom masks
+5. Test masks on diverse slides
+
+### Tile Extraction
+1. **Always preview with `locate_tiles()` before extracting**
+2. Choose appropriate tiler:
+   - RandomTiler: Sampling and exploration
+   - GridTiler: Complete coverage
+   - ScoreTiler: Quality-driven selection
+3. Set appropriate `tissue_percent` threshold (70-90% typical)
+4. Use seeds for reproducibility in RandomTiler
+5. Extract at appropriate pyramid level for analysis resolution
+6. Enable logging for large datasets
+
+### Performance
+1. Extract at lower levels (1, 2) for faster processing
+2. Use `BiggestTissueBoxMask` over `TissueMask` when appropriate
+3. Adjust `tissue_percent` to reduce invalid tile attempts
+4. Limit `n_tiles` for initial exploration
+5. Use `pixel_overlap=0` for non-overlapping grids
+
+### Quality Control
+1. Validate tile quality (check for blur, artifacts, focus)
+2. Review score distributions for ScoreTiler
+3. Inspect top and bottom scoring tiles
+4. Monitor tissue coverage statistics
+5. Filter extracted tiles by additional quality metrics if needed
+
+## Common Use Cases
+
+### Training Deep Learning Models
+- Extract balanced datasets using RandomTiler across multiple slides
+- Use ScoreTiler with NucleiScorer to focus on cell-rich regions
+- Extract at consistent resolution (level 0 or level 1)
+- Generate CSV reports for tracking tile metadata
+
+### Whole Slide Analysis
+- Use GridTiler for complete tissue coverage
+- Extract at multiple pyramid levels for hierarchical analysis
+- Maintain spatial relationships with grid positions
+- Use `pixel_overlap` for sliding window approaches
+
+### Tissue Characterization
+- Sample diverse regions with RandomTiler
+- Quantify tissue coverage with masks
+- Extract stain-specific information with HED decomposition
+- Compare tissue patterns across slides
+
+### Quality Assessment
+- Identify optimal focus regions with ScoreTiler
+- Detect artifacts using custom masks and filters
+- Assess staining quality across slide collection
+- Flag problematic slides for manual review
+
+### Dataset Curation
+- Use ScoreTiler to prioritize informative tiles
+- Filter tiles by tissue percentage
+- Generate reports with tile scores and metadata
+- Create stratified datasets across slides and tissue types
+
+## Troubleshooting
+
+### No tiles extracted
+- Lower `tissue_percent` threshold
+- Verify slide contains tissue (check thumbnail)
+- Ensure extraction_mask captures tissue regions
+- Check tile_size is appropriate for slide resolution
+
+### Many background tiles
+- Enable `check_tissue=True`
+- Increase `tissue_percent` threshold
+- Use appropriate mask (TissueMask vs BiggestTissueBoxMask)
+- Customize mask filters to better detect tissue
+
+### Extraction very slow
+- Extract at lower pyramid level (level=1 or 2)
+- Reduce `n_tiles` for RandomTiler/ScoreTiler
+- Use RandomTiler instead of GridTiler for sampling
+- Use BiggestTissueBoxMask instead of TissueMask
+
+### Tiles have artifacts
+- Implement custom annotation-exclusion masks
+- Adjust filter parameters for artifact removal
+- Increase small object removal threshold
+- Apply post-extraction quality filtering
+
+### Inconsistent results across slides
+- Use same seed for RandomTiler
+- Normalize staining with preprocessing filters
+- Adjust `tissue_percent` per staining quality
+- Implement slide-specific mask customization
+
+## Resources
+
+This skill includes detailed reference documentation in the `references/` directory:
+
+### references/slide_management.md
+Comprehensive guide to loading, inspecting, and working with whole slide images:
+- Slide initialization and configuration
+- Built-in sample datasets
+- Slide properties and metadata
+- Thumbnail generation and visualization
+- Working with pyramid levels
+- Multi-slide processing workflows
+- Best practices and common patterns
+
+### references/tissue_masks.md
+Complete documentation on tissue detection and masking:
+- TissueMask, BiggestTissueBoxMask, BinaryMask classes
+- How tissue detection filters work
+- Customizing masks with filter chains
+- Visualizing masks
+- Creating custom rectangular and annotation-exclusion masks
+- Integration with tile extraction
+- Best practices and troubleshooting
+
+### references/tile_extraction.md
+Detailed explanation of tile extraction strategies:
+- RandomTiler, GridTiler, ScoreTiler comparison
+- Available scorers (NucleiScorer, CellularityScorer, custom)
+- Common and strategy-specific parameters
+- Tile preview with locate_tiles()
+- Extraction workflows and CSV reporting
+- Advanced patterns (multi-level, hierarchical)
+- Performance optimization
+- Troubleshooting common issues
+
+### references/filters_preprocessing.md
+Complete filter reference and preprocessing guide:
+- Image filters (color conversion, thresholding, contrast)
+- Morphological filters (dilation, erosion, opening, closing)
+- Filter composition and chaining
+- Common preprocessing pipelines
+- Applying filters to tiles
+- Custom mask filters
+- Quality control filters
+- Best practices and troubleshooting
+
+### references/visualization.md
+Comprehensive visualization guide:
+- Slide thumbnail display and saving
+- Mask visualization techniques
+- Tile location preview
+- Displaying extracted tiles and creating mosaics
+- Quality assessment visualizations
+- Multi-slide comparison
+- Filter effect visualization
+- Exporting high-resolution figures and PDFs
+- Interactive visualization in Jupyter notebooks
+
+**Usage pattern:** Reference files contain in-depth information to support workflows described in this main skill document. Load specific reference files as needed for detailed implementation guidance, troubleshooting, or advanced features.

skills/histolab/references/filters_preprocessing.md

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+# Filters and Preprocessing
+
+## Overview
+
+Histolab provides a comprehensive set of filters for preprocessing whole slide images and tiles. Filters can be applied to images for visualization, quality control, tissue detection, and artifact removal. They are composable and can be chained together to create sophisticated preprocessing pipelines.
+
+## Filter Categories
+
+### Image Filters
+Color space conversions, thresholding, and intensity adjustments
+
+### Morphological Filters
+Structural operations like dilation, erosion, opening, and closing
+
+### Composition Filters
+Utilities for combining multiple filters
+
+## Image Filters
+
+### RgbToGrayscale
+
+Convert RGB images to grayscale.
+
+```python
+from histolab.filters.image_filters import RgbToGrayscale
+
+gray_filter = RgbToGrayscale()
+gray_image = gray_filter(rgb_image)
+```
+
+**Use cases:**
+- Preprocessing for intensity-based operations
+- Simplifying color complexity
+- Input for morphological operations
+
+### RgbToHsv
+
+Convert RGB to HSV (Hue, Saturation, Value) color space.
+
+```python
+from histolab.filters.image_filters import RgbToHsv
+
+hsv_filter = RgbToHsv()
+hsv_image = hsv_filter(rgb_image)
+```
+
+**Use cases:**
+- Color-based tissue segmentation
+- Detecting pen markings by hue
+- Separating chromatic from achromatic content
+
+### RgbToHed
+
+Convert RGB to HED (Hematoxylin-Eosin-DAB) color space for stain deconvolution.
+
+```python
+from histolab.filters.image_filters import RgbToHed
+
+hed_filter = RgbToHed()
+hed_image = hed_filter(rgb_image)
+```
+
+**Use cases:**
+- Separating H&E stain components
+- Analyzing nuclear (hematoxylin) vs. cytoplasmic (eosin) staining
+- Quantifying stain intensity
+
+### OtsuThreshold
+
+Apply Otsu's automatic thresholding method to create binary images.
+
+```python
+from histolab.filters.image_filters import OtsuThreshold
+
+otsu_filter = OtsuThreshold()
+binary_image = otsu_filter(grayscale_image)
+```
+
+**How it works:**
+- Automatically determines optimal threshold
+- Separates foreground from background
+- Minimizes intra-class variance
+
+**Use cases:**
+- Tissue detection
+- Nuclei segmentation
+- Binary mask creation
+
+### AdaptiveThreshold
+
+Apply adaptive thresholding for local intensity variations.
+
+```python
+from histolab.filters.image_filters import AdaptiveThreshold
+
+adaptive_filter = AdaptiveThreshold(
+    block_size=11,      # Size of local neighborhood
+    offset=2            # Constant subtracted from mean
+)
+binary_image = adaptive_filter(grayscale_image)
+```
+
+**Use cases:**
+- Non-uniform illumination
+- Local contrast enhancement
+- Handling variable staining intensity
+
+### Invert
+
+Invert image intensity values.
+
+```python
+from histolab.filters.image_filters import Invert
+
+invert_filter = Invert()
+inverted_image = invert_filter(image)
+```
+
+**Use cases:**
+- Preprocessing for certain segmentation algorithms
+- Visualization adjustments
+
+### StretchContrast
+
+Enhance image contrast by stretching intensity range.
+
+```python
+from histolab.filters.image_filters import StretchContrast
+
+contrast_filter = StretchContrast()
+enhanced_image = contrast_filter(image)
+```
+
+**Use cases:**
+- Improving visibility of low-contrast features
+- Preprocessing for visualization
+- Enhancing faint structures
+
+### HistogramEqualization
+
+Equalize image histogram for contrast enhancement.
+
+```python
+from histolab.filters.image_filters import HistogramEqualization
+
+hist_eq_filter = HistogramEqualization()
+equalized_image = hist_eq_filter(grayscale_image)
+```
+
+**Use cases:**
+- Standardizing image contrast
+- Revealing hidden details
+- Preprocessing for feature extraction
+
+## Morphological Filters
+
+### BinaryDilation
+
+Expand white regions in binary images.
+
+```python
+from histolab.filters.morphological_filters import BinaryDilation
+
+dilation_filter = BinaryDilation(disk_size=5)
+dilated_image = dilation_filter(binary_image)
+```
+
+**Parameters:**
+- `disk_size`: Size of structuring element (default: 5)
+
+**Use cases:**
+- Connecting nearby tissue regions
+- Filling small gaps
+- Expanding tissue masks
+
+### BinaryErosion
+
+Shrink white regions in binary images.
+
+```python
+from histolab.filters.morphological_filters import BinaryErosion
+
+erosion_filter = BinaryErosion(disk_size=5)
+eroded_image = erosion_filter(binary_image)
+```
+
+**Use cases:**
+- Removing small protrusions
+- Separating connected objects
+- Shrinking tissue boundaries
+
+### BinaryOpening
+
+Erosion followed by dilation (removes small objects).
+
+```python
+from histolab.filters.morphological_filters import BinaryOpening
+
+opening_filter = BinaryOpening(disk_size=3)
+opened_image = opening_filter(binary_image)
+```
+
+**Use cases:**
+- Removing small artifacts
+- Smoothing object boundaries
+- Noise reduction
+
+### BinaryClosing
+
+Dilation followed by erosion (fills small holes).
+
+```python
+from histolab.filters.morphological_filters import BinaryClosing
+
+closing_filter = BinaryClosing(disk_size=5)
+closed_image = closing_filter(binary_image)
+```
+
+**Use cases:**
+- Filling small holes in tissue regions
+- Connecting nearby objects
+- Smoothing internal boundaries
+
+### RemoveSmallObjects
+
+Remove connected components smaller than a threshold.
+
+```python
+from histolab.filters.morphological_filters import RemoveSmallObjects
+
+remove_small_filter = RemoveSmallObjects(
+    area_threshold=500  # Minimum area in pixels
+)
+cleaned_image = remove_small_filter(binary_image)
+```
+
+**Use cases:**
+- Removing dust and artifacts
+- Filtering noise
+- Cleaning tissue masks
+
+### RemoveSmallHoles
+
+Fill holes smaller than a threshold.
+
+```python
+from histolab.filters.morphological_filters import RemoveSmallHoles
+
+fill_holes_filter = RemoveSmallHoles(
+    area_threshold=1000  # Maximum hole size to fill
+)
+filled_image = fill_holes_filter(binary_image)
+```
+
+**Use cases:**
+- Filling small gaps in tissue
+- Creating continuous tissue regions
+- Removing internal artifacts
+
+## Filter Composition
+
+### Chaining Filters
+
+Combine multiple filters in sequence:
+
+```python
+from histolab.filters.image_filters import RgbToGrayscale, OtsuThreshold
+from histolab.filters.morphological_filters import BinaryDilation, RemoveSmallObjects
+from histolab.filters.compositions import Compose
+
+# Create filter pipeline
+tissue_detection_pipeline = Compose([
+    RgbToGrayscale(),
+    OtsuThreshold(),
+    BinaryDilation(disk_size=5),
+    RemoveSmallHoles(area_threshold=1000),
+    RemoveSmallObjects(area_threshold=500)
+])
+
+# Apply pipeline
+result = tissue_detection_pipeline(rgb_image)
+```
+
+### Lambda Filters
+
+Create custom filters inline:
+
+```python
+from histolab.filters.image_filters import Lambda
+import numpy as np
+
+# Custom brightness adjustment
+brightness_filter = Lambda(lambda img: np.clip(img * 1.2, 0, 255).astype(np.uint8))
+
+# Custom color channel extraction
+red_channel_filter = Lambda(lambda img: img[:, :, 0])
+```
+
+## Common Preprocessing Pipelines
+
+### Standard Tissue Detection
+
+```python
+from histolab.filters.compositions import Compose
+from histolab.filters.image_filters import RgbToGrayscale, OtsuThreshold
+from histolab.filters.morphological_filters import (
+    BinaryDilation, RemoveSmallHoles, RemoveSmallObjects
+)
+
+tissue_detection = Compose([
+    RgbToGrayscale(),
+    OtsuThreshold(),
+    BinaryDilation(disk_size=5),
+    RemoveSmallHoles(area_threshold=1000),
+    RemoveSmallObjects(area_threshold=500)
+])
+```
+
+### Pen Mark Removal
+
+```python
+from histolab.filters.image_filters import RgbToHsv, Lambda
+import numpy as np
+
+def remove_pen_marks(hsv_image):
+    """Remove blue/green pen markings."""
+    h, s, v = hsv_image[:, :, 0], hsv_image[:, :, 1], hsv_image[:, :, 2]
+    # Mask for blue/green hues (common pen colors)
+    pen_mask = ((h > 0.45) & (h < 0.7) & (s > 0.3))
+    # Set pen regions to white
+    hsv_image[pen_mask] = [0, 0, 1]
+    return hsv_image
+
+pen_removal = Compose([
+    RgbToHsv(),
+    Lambda(remove_pen_marks)
+])
+```
+
+### Nuclei Enhancement
+
+```python
+from histolab.filters.image_filters import RgbToHed, HistogramEqualization
+from histolab.filters.compositions import Compose
+
+nuclei_enhancement = Compose([
+    RgbToHed(),
+    Lambda(lambda hed: hed[:, :, 0]),  # Extract hematoxylin channel
+    HistogramEqualization()
+])
+```
+
+### Contrast Normalization
+
+```python
+from histolab.filters.image_filters import StretchContrast, HistogramEqualization
+
+contrast_normalization = Compose([
+    RgbToGrayscale(),
+    StretchContrast(),
+    HistogramEqualization()
+])
+```
+
+## Applying Filters to Tiles
+
+Filters can be applied to individual tiles:
+
+```python
+from histolab.tile import Tile
+from histolab.filters.image_filters import RgbToGrayscale
+
+# Load or extract tile
+tile = Tile(image=pil_image, coords=(x, y))
+
+# Apply filter
+gray_filter = RgbToGrayscale()
+filtered_tile = tile.apply_filters(gray_filter)
+
+# Chain multiple filters
+from histolab.filters.compositions import Compose
+from histolab.filters.image_filters import StretchContrast
+
+filter_chain = Compose([
+    RgbToGrayscale(),
+    StretchContrast()
+])
+processed_tile = tile.apply_filters(filter_chain)
+```
+
+## Custom Mask Filters
+
+Integrate custom filters with tissue masks:
+
+```python
+from histolab.masks import TissueMask
+from histolab.filters.compositions import Compose
+from histolab.filters.image_filters import RgbToGrayscale, OtsuThreshold
+from histolab.filters.morphological_filters import BinaryDilation
+
+# Custom aggressive tissue detection
+aggressive_filters = Compose([
+    RgbToGrayscale(),
+    OtsuThreshold(),
+    BinaryDilation(disk_size=10),  # Larger dilation
+    RemoveSmallObjects(area_threshold=5000)  # Remove only large artifacts
+])
+
+# Create mask with custom filters
+custom_mask = TissueMask(filters=aggressive_filters)
+```
+
+## Stain Normalization
+
+While histolab doesn't have built-in stain normalization, filters can be used for basic normalization:
+
+```python
+from histolab.filters.image_filters import RgbToHed, Lambda
+import numpy as np
+
+def normalize_hed(hed_image, target_means=[0.65, 0.70], target_stds=[0.15, 0.13]):
+    """Simple H&E normalization."""
+    h_channel = hed_image[:, :, 0]
+    e_channel = hed_image[:, :, 1]
+
+    # Normalize hematoxylin
+    h_normalized = (h_channel - h_channel.mean()) / h_channel.std()
+    h_normalized = h_normalized * target_stds[0] + target_means[0]
+
+    # Normalize eosin
+    e_normalized = (e_channel - e_channel.mean()) / e_channel.std()
+    e_normalized = e_normalized * target_stds[1] + target_means[1]
+
+    hed_image[:, :, 0] = h_normalized
+    hed_image[:, :, 1] = e_normalized
+
+    return hed_image
+
+normalization_pipeline = Compose([
+    RgbToHed(),
+    Lambda(normalize_hed)
+    # Convert back to RGB if needed
+])
+```
+
+## Best Practices
+
+1. **Preview filters**: Visualize filter outputs on thumbnails before applying to tiles
+2. **Chain efficiently**: Order filters logically (e.g., color conversion before thresholding)
+3. **Tune parameters**: Adjust thresholds and structuring element sizes for specific tissues
+4. **Use composition**: Build reusable filter pipelines with `Compose`
+5. **Consider performance**: Complex filter chains increase processing time
+6. **Validate on diverse slides**: Test filters across different scanners, stains, and tissue types
+7. **Document custom filters**: Clearly describe purpose and parameters of custom pipelines
+
+## Quality Control Filters
+
+### Blur Detection
+
+```python
+from histolab.filters.image_filters import Lambda
+import cv2
+import numpy as np
+
+def laplacian_blur_score(gray_image):
+    """Calculate Laplacian variance (blur metric)."""
+    return cv2.Laplacian(np.array(gray_image), cv2.CV_64F).var()
+
+blur_detector = Lambda(lambda img: laplacian_blur_score(
+    RgbToGrayscale()(img)
+))
+```
+
+### Tissue Coverage
+
+```python
+from histolab.filters.image_filters import RgbToGrayscale, OtsuThreshold
+from histolab.filters.compositions import Compose
+
+def tissue_coverage(image):
+    """Calculate percentage of tissue in image."""
+    tissue_mask = Compose([
+        RgbToGrayscale(),
+        OtsuThreshold()
+    ])(image)
+    return tissue_mask.sum() / tissue_mask.size * 100
+
+coverage_filter = Lambda(tissue_coverage)
+```
+
+## Troubleshooting
+
+### Issue: Tissue detection misses valid tissue
+**Solutions:**
+- Reduce `area_threshold` in `RemoveSmallObjects`
+- Decrease erosion/opening disk size
+- Try adaptive thresholding instead of Otsu
+
+### Issue: Too many artifacts included
+**Solutions:**
+- Increase `area_threshold` in `RemoveSmallObjects`
+- Add opening/closing operations
+- Use custom color-based filtering for specific artifacts
+
+### Issue: Tissue boundaries too rough
+**Solutions:**
+- Add `BinaryClosing` or `BinaryOpening` for smoothing
+- Adjust disk_size for morphological operations
+
+### Issue: Variable staining quality
+**Solutions:**
+- Apply histogram equalization
+- Use adaptive thresholding
+- Implement stain normalization pipeline

skills/histolab/references/slide_management.md

@@ -0,0 +1,172 @@
+# Slide Management
+
+## Overview
+
+The `Slide` class is the primary interface for working with whole slide images (WSI) in histolab. It provides methods to load, inspect, and process large histopathology images stored in various formats.
+
+## Initialization
+
+```python
+from histolab.slide import Slide
+
+# Initialize a slide with a WSI file and output directory
+slide = Slide(processed_path="path/to/processed/output",
+              slide_path="path/to/slide.svs")
+```
+
+**Parameters:**
+- `slide_path`: Path to the whole slide image file (supports multiple formats: SVS, TIFF, NDPI, etc.)
+- `processed_path`: Directory where processed outputs (tiles, thumbnails, etc.) will be saved
+
+## Loading Sample Data
+
+Histolab provides built-in sample datasets from TCGA for testing and demonstration:
+
+```python
+from histolab.data import prostate_tissue, ovarian_tissue, breast_tissue, heart_tissue, kidney_tissue
+
+# Load prostate tissue sample
+prostate_svs, prostate_path = prostate_tissue()
+slide = Slide(prostate_path, processed_path="output/")
+```
+
+Available sample datasets:
+- `prostate_tissue()`: Prostate tissue sample
+- `ovarian_tissue()`: Ovarian tissue sample
+- `breast_tissue()`: Breast tissue sample
+- `heart_tissue()`: Heart tissue sample
+- `kidney_tissue()`: Kidney tissue sample
+
+## Key Properties
+
+### Slide Dimensions
+```python
+# Get slide dimensions at level 0 (highest resolution)
+width, height = slide.dimensions
+
+# Get dimensions at specific pyramid level
+level_dimensions = slide.level_dimensions
+# Returns tuple of (width, height) for each level
+```
+
+### Magnification Information
+```python
+# Get base magnification (e.g., 40x, 20x)
+base_mag = slide.base_mpp  # Microns per pixel at level 0
+
+# Get all available levels
+num_levels = slide.levels  # Number of pyramid levels
+```
+
+### Slide Properties
+```python
+# Access OpenSlide properties dictionary
+properties = slide.properties
+
+# Common properties include:
+# - slide.properties['openslide.objective-power']: Objective power
+# - slide.properties['openslide.mpp-x']: Microns per pixel in X
+# - slide.properties['openslide.mpp-y']: Microns per pixel in Y
+# - slide.properties['openslide.vendor']: Scanner vendor
+```
+
+## Thumbnail Generation
+
+```python
+# Get thumbnail at specific size
+thumbnail = slide.thumbnail
+
+# Save thumbnail to disk
+slide.save_thumbnail()  # Saves to processed_path
+
+# Get scaled thumbnail
+scaled_thumbnail = slide.scaled_image(scale_factor=32)
+```
+
+## Slide Visualization
+
+```python
+# Display slide thumbnail with matplotlib
+import matplotlib.pyplot as plt
+
+plt.figure(figsize=(10, 10))
+plt.imshow(slide.thumbnail)
+plt.title(f"Slide: {slide.name}")
+plt.axis('off')
+plt.show()
+```
+
+## Extracting Regions
+
+```python
+# Extract region at specific coordinates and level
+region = slide.extract_region(
+    location=(x, y),  # Top-left coordinates at level 0
+    size=(width, height),  # Region size
+    level=0  # Pyramid level
+)
+```
+
+## Working with Pyramid Levels
+
+WSI files use a pyramidal structure with multiple resolution levels:
+- Level 0: Highest resolution (native scan resolution)
+- Level 1+: Progressively lower resolutions for faster access
+
+```python
+# Check available levels
+for level in range(slide.levels):
+    dims = slide.level_dimensions[level]
+    downsample = slide.level_downsamples[level]
+    print(f"Level {level}: {dims}, downsample: {downsample}x")
+```
+
+## Slide Name and Path
+
+```python
+# Get slide filename without extension
+slide_name = slide.name
+
+# Get full path to slide file
+slide_path = slide.scaled_image
+```
+
+## Best Practices
+
+1. **Always specify processed_path**: Organize outputs in dedicated directories
+2. **Check dimensions before processing**: Large slides can exceed memory limits
+3. **Use appropriate pyramid levels**: Extract tiles at levels matching your analysis resolution
+4. **Preview with thumbnails**: Use thumbnails for quick visualization before heavy processing
+5. **Monitor memory usage**: Level 0 operations on large slides require significant RAM
+
+## Common Workflows
+
+### Slide Inspection Workflow
+```python
+from histolab.slide import Slide
+
+# Load slide
+slide = Slide("slide.svs", processed_path="output/")
+
+# Inspect properties
+print(f"Dimensions: {slide.dimensions}")
+print(f"Levels: {slide.levels}")
+print(f"Magnification: {slide.properties.get('openslide.objective-power', 'N/A')}")
+
+# Save thumbnail for review
+slide.save_thumbnail()
+```
+
+### Multi-Slide Processing
+```python
+import os
+from pathlib import Path
+
+slide_dir = Path("slides/")
+output_dir = Path("processed/")
+
+for slide_path in slide_dir.glob("*.svs"):
+    slide = Slide(slide_path, processed_path=output_dir / slide_path.stem)
+    # Process each slide
+    print(f"Processing: {slide.name}")
+```

skills/histolab/references/tile_extraction.md

@@ -0,0 +1,421 @@
+# Tile Extraction
+
+## Overview
+
+Tile extraction is the process of cropping smaller, manageable regions from large whole slide images. Histolab provides three main extraction strategies, each suited for different analysis needs. All tilers share common parameters and provide methods for previewing and extracting tiles.
+
+## Common Parameters
+
+All tiler classes accept these parameters:
+
+```python
+tile_size: tuple = (512, 512)           # Tile dimensions in pixels (width, height)
+level: int = 0                          # Pyramid level for extraction (0=highest resolution)
+check_tissue: bool = True               # Filter tiles by tissue content
+tissue_percent: float = 80.0            # Minimum tissue coverage (0-100)
+pixel_overlap: int = 0                  # Overlap between adjacent tiles (GridTiler only)
+prefix: str = ""                        # Prefix for saved tile filenames
+suffix: str = ".png"                    # File extension for saved tiles
+extraction_mask: BinaryMask = BiggestTissueBoxMask()  # Mask defining extraction region
+```
+
+## RandomTiler
+
+**Purpose:** Extract a fixed number of randomly positioned tiles from tissue regions.
+
+```python
+from histolab.tiler import RandomTiler
+
+random_tiler = RandomTiler(
+    tile_size=(512, 512),
+    n_tiles=100,                # Number of random tiles to extract
+    level=0,
+    seed=42,                    # Random seed for reproducibility
+    check_tissue=True,
+    tissue_percent=80.0
+)
+
+# Extract tiles
+random_tiler.extract(slide, extraction_mask=TissueMask())
+```
+
+**Key Parameters:**
+- `n_tiles`: Number of random tiles to extract
+- `seed`: Random seed for reproducible tile selection
+- `max_iter`: Maximum attempts to find valid tiles (default 1000)
+
+**Use cases:**
+- Exploratory analysis of slide content
+- Sampling diverse regions for training data
+- Quick assessment of tissue characteristics
+- Balanced dataset creation from multiple slides
+
+**Advantages:**
+- Computationally efficient
+- Good for sampling diverse tissue morphologies
+- Reproducible with seed parameter
+- Fast execution
+
+**Limitations:**
+- May miss rare tissue patterns
+- No guarantee of coverage
+- Random distribution may not capture structured features
+
+## GridTiler
+
+**Purpose:** Extract tiles systematically across tissue regions following a grid pattern.
+
+```python
+from histolab.tiler import GridTiler
+
+grid_tiler = GridTiler(
+    tile_size=(512, 512),
+    level=0,
+    check_tissue=True,
+    tissue_percent=80.0,
+    pixel_overlap=0             # Overlap in pixels between adjacent tiles
+)
+
+# Extract tiles
+grid_tiler.extract(slide)
+```
+
+**Key Parameters:**
+- `pixel_overlap`: Number of overlapping pixels between adjacent tiles
+  - `pixel_overlap=0`: Non-overlapping tiles
+  - `pixel_overlap=128`: 128-pixel overlap on each side
+  - Can be used for sliding window approaches
+
+**Use cases:**
+- Comprehensive slide coverage
+- Spatial analysis requiring positional information
+- Image reconstruction from tiles
+- Semantic segmentation tasks
+- Region-based analysis
+
+**Advantages:**
+- Complete tissue coverage
+- Preserves spatial relationships
+- Predictable tile positions
+- Suitable for whole-slide analysis
+
+**Limitations:**
+- Computationally intensive for large slides
+- May generate many background-heavy tiles (mitigated by `check_tissue`)
+- Larger output datasets
+
+**Grid Pattern:**
+```
+[Tile 1][Tile 2][Tile 3]
+[Tile 4][Tile 5][Tile 6]
+[Tile 7][Tile 8][Tile 9]
+```
+
+With `pixel_overlap=64`:
+```
+[Tile 1-overlap-Tile 2-overlap-Tile 3]
+[    overlap       overlap       overlap]
+[Tile 4-overlap-Tile 5-overlap-Tile 6]
+```
+
+## ScoreTiler
+
+**Purpose:** Extract top-ranked tiles based on custom scoring functions.
+
+```python
+from histolab.tiler import ScoreTiler
+from histolab.scorer import NucleiScorer
+
+score_tiler = ScoreTiler(
+    tile_size=(512, 512),
+    n_tiles=50,                 # Number of top-scoring tiles to extract
+    level=0,
+    scorer=NucleiScorer(),      # Scoring function
+    check_tissue=True
+)
+
+# Extract top-scoring tiles
+score_tiler.extract(slide)
+```
+
+**Key Parameters:**
+- `n_tiles`: Number of top-scoring tiles to extract
+- `scorer`: Scoring function (e.g., `NucleiScorer`, `CellularityScorer`, custom scorer)
+
+**Use cases:**
+- Extracting most informative regions
+- Prioritizing tiles with specific features (nuclei, cells, etc.)
+- Quality-based tile selection
+- Focusing on diagnostically relevant areas
+- Training data curation
+
+**Advantages:**
+- Focuses on most informative tiles
+- Reduces dataset size while maintaining quality
+- Customizable with different scorers
+- Efficient for targeted analysis
+
+**Limitations:**
+- Slower than RandomTiler (must score all candidate tiles)
+- Requires appropriate scorer for task
+- May miss low-scoring but relevant regions
+
+## Available Scorers
+
+### NucleiScorer
+
+Scores tiles based on nuclei detection and density.
+
+```python
+from histolab.scorer import NucleiScorer
+
+nuclei_scorer = NucleiScorer()
+```
+
+**How it works:**
+1. Converts tile to grayscale
+2. Applies thresholding to detect nuclei
+3. Counts nuclei-like structures
+4. Assigns score based on nuclei density
+
+**Best for:**
+- Cell-rich tissue regions
+- Tumor detection
+- Mitosis analysis
+- Areas with high cellular content
+
+### CellularityScorer
+
+Scores tiles based on overall cellular content.
+
+```python
+from histolab.scorer import CellularityScorer
+
+cellularity_scorer = CellularityScorer()
+```
+
+**Best for:**
+- Identifying cellular vs. stromal regions
+- Tumor cellularity assessment
+- Separating dense from sparse tissue areas
+
+### Custom Scorers
+
+Create custom scoring functions for specific needs:
+
+```python
+from histolab.scorer import Scorer
+import numpy as np
+
+class ColorVarianceScorer(Scorer):
+    def __call__(self, tile):
+        """Score tiles based on color variance."""
+        tile_array = np.array(tile.image)
+        # Calculate color variance
+        variance = np.var(tile_array, axis=(0, 1)).sum()
+        return variance
+
+# Use custom scorer
+variance_scorer = ColorVarianceScorer()
+score_tiler = ScoreTiler(
+    tile_size=(512, 512),
+    n_tiles=30,
+    scorer=variance_scorer
+)
+```
+
+## Tile Preview with locate_tiles()
+
+Preview tile locations before extraction to validate tiler configuration:
+
+```python
+# Preview random tile locations
+random_tiler.locate_tiles(
+    slide=slide,
+    extraction_mask=TissueMask(),
+    n_tiles=20  # Number of tiles to preview (for RandomTiler)
+)
+```
+
+This displays the slide thumbnail with colored rectangles indicating tile positions.
+
+## Extraction Workflow
+
+### Basic Extraction
+
+```python
+from histolab.slide import Slide
+from histolab.tiler import RandomTiler
+
+# Load slide
+slide = Slide("slide.svs", processed_path="output/tiles/")
+
+# Configure tiler
+tiler = RandomTiler(
+    tile_size=(512, 512),
+    n_tiles=100,
+    level=0,
+    seed=42
+)
+
+# Extract tiles (saved to processed_path)
+tiler.extract(slide)
+```
+
+### Extraction with Logging
+
+```python
+import logging
+
+# Enable logging
+logging.basicConfig(level=logging.INFO)
+
+# Extract tiles with progress information
+tiler.extract(slide)
+# Output: INFO: Tile 1/100 saved...
+# Output: INFO: Tile 2/100 saved...
+```
+
+### Extraction with Report
+
+```python
+# Generate CSV report with tile information
+score_tiler = ScoreTiler(
+    tile_size=(512, 512),
+    n_tiles=50,
+    scorer=NucleiScorer()
+)
+
+# Extract and save report
+score_tiler.extract(slide, report_path="tiles_report.csv")
+
+# Report contains: tile name, coordinates, score, tissue percentage
+```
+
+Report format:
+```csv
+tile_name,x_coord,y_coord,level,score,tissue_percent
+tile_001.png,10240,5120,0,0.89,95.2
+tile_002.png,15360,7680,0,0.85,91.7
+...
+```
+
+## Advanced Extraction Patterns
+
+### Multi-Level Extraction
+
+Extract tiles at different magnification levels:
+
+```python
+# High resolution tiles (level 0)
+high_res_tiler = RandomTiler(tile_size=(512, 512), n_tiles=50, level=0)
+high_res_tiler.extract(slide)
+
+# Medium resolution tiles (level 1)
+med_res_tiler = RandomTiler(tile_size=(512, 512), n_tiles=50, level=1)
+med_res_tiler.extract(slide)
+
+# Low resolution tiles (level 2)
+low_res_tiler = RandomTiler(tile_size=(512, 512), n_tiles=50, level=2)
+low_res_tiler.extract(slide)
+```
+
+### Hierarchical Extraction
+
+Extract at multiple scales from same locations:
+
+```python
+# Extract random locations at level 0
+random_tiler_l0 = RandomTiler(
+    tile_size=(512, 512),
+    n_tiles=30,
+    level=0,
+    seed=42,
+    prefix="level0_"
+)
+random_tiler_l0.extract(slide)
+
+# Extract same locations at level 1 (use same seed)
+random_tiler_l1 = RandomTiler(
+    tile_size=(512, 512),
+    n_tiles=30,
+    level=1,
+    seed=42,
+    prefix="level1_"
+)
+random_tiler_l1.extract(slide)
+```
+
+### Custom Tile Filtering
+
+Apply additional filtering after extraction:
+
+```python
+from PIL import Image
+import numpy as np
+from pathlib import Path
+
+def filter_blurry_tiles(tile_dir, threshold=100):
+    """Remove blurry tiles using Laplacian variance."""
+    for tile_path in Path(tile_dir).glob("*.png"):
+        img = Image.open(tile_path)
+        gray = np.array(img.convert('L'))
+        laplacian_var = cv2.Laplacian(gray, cv2.CV_64F).var()
+
+        if laplacian_var < threshold:
+            tile_path.unlink()  # Remove blurry tile
+            print(f"Removed blurry tile: {tile_path.name}")
+
+# Use after extraction
+tiler.extract(slide)
+filter_blurry_tiles("output/tiles/")
+```
+
+## Best Practices
+
+1. **Preview before extraction**: Always use `locate_tiles()` to verify tile placement
+2. **Use appropriate level**: Match extraction level to analysis resolution requirements
+3. **Set tissue_percent threshold**: Adjust based on staining and tissue type (70-90% typical)
+4. **Choose right tiler**:
+   - RandomTiler for sampling and exploration
+   - GridTiler for comprehensive coverage
+   - ScoreTiler for targeted, quality-driven extraction
+5. **Enable logging**: Monitor extraction progress for large datasets
+6. **Use seeds for reproducibility**: Set random seeds in RandomTiler
+7. **Consider storage**: GridTiler can generate thousands of tiles per slide
+8. **Validate tile quality**: Check extracted tiles for artifacts, blur, or focus issues
+
+## Performance Optimization
+
+1. **Extract at appropriate level**: Lower levels (1, 2) extract faster
+2. **Adjust tissue_percent**: Higher thresholds reduce invalid tile attempts
+3. **Use BiggestTissueBoxMask**: Faster than TissueMask for single tissue sections
+4. **Limit n_tiles**: For RandomTiler and ScoreTiler
+5. **Use pixel_overlap=0**: For non-overlapping GridTiler extraction
+
+## Troubleshooting
+
+### Issue: No tiles extracted
+**Solutions:**
+- Lower `tissue_percent` threshold
+- Verify slide contains tissue (check thumbnail)
+- Ensure extraction_mask captures tissue regions
+- Check that tile_size is appropriate for slide resolution
+
+### Issue: Many background tiles extracted
+**Solutions:**
+- Enable `check_tissue=True`
+- Increase `tissue_percent` threshold
+- Use appropriate mask (TissueMask vs. BiggestTissueBoxMask)
+
+### Issue: Extraction is very slow
+**Solutions:**
+- Extract at lower pyramid level (level=1 or 2)
+- Reduce `n_tiles` for RandomTiler/ScoreTiler
+- Use RandomTiler instead of GridTiler for sampling
+- Use BiggestTissueBoxMask instead of TissueMask
+
+### Issue: Tiles have too much overlap (GridTiler)
+**Solutions:**
+- Set `pixel_overlap=0` for non-overlapping tiles
+- Reduce `pixel_overlap` value

skills/histolab/references/tissue_masks.md

@@ -0,0 +1,251 @@
+# Tissue Masks
+
+## Overview
+
+Tissue masks are binary representations that identify tissue regions within whole slide images. They are essential for filtering out background, artifacts, and non-tissue areas during tile extraction. Histolab provides several mask classes to accommodate different tissue segmentation needs.
+
+## Mask Classes
+
+### BinaryMask
+
+**Purpose:** Generic base class for creating custom binary masks.
+
+```python
+from histolab.masks import BinaryMask
+
+class CustomMask(BinaryMask):
+    def _mask(self, obj):
+        # Implement custom masking logic
+        # Return binary numpy array
+        pass
+```
+
+**Use cases:**
+- Custom tissue segmentation algorithms
+- Region-specific analysis (e.g., excluding annotations)
+- Integration with external segmentation models
+
+### TissueMask
+
+**Purpose:** Segments all tissue regions in the slide using automated filters.
+
+```python
+from histolab.masks import TissueMask
+
+# Create tissue mask
+tissue_mask = TissueMask()
+
+# Apply to slide
+mask_array = tissue_mask(slide)
+```
+
+**How it works:**
+1. Converts image to grayscale
+2. Applies Otsu thresholding to separate tissue from background
+3. Performs binary dilation to connect nearby tissue regions
+4. Removes small holes within tissue regions
+5. Filters out small objects (artifacts)
+
+**Returns:** Binary NumPy array where:
+- `True` (or 1): Tissue pixels
+- `False` (or 0): Background pixels
+
+**Best for:**
+- Slides with multiple separate tissue sections
+- Comprehensive tissue analysis
+- When all tissue regions are important
+
+### BiggestTissueBoxMask (Default)
+
+**Purpose:** Identifies and returns the bounding box of the largest connected tissue region.
+
+```python
+from histolab.masks import BiggestTissueBoxMask
+
+# Create mask for largest tissue region
+biggest_mask = BiggestTissueBoxMask()
+
+# Apply to slide
+mask_array = biggest_mask(slide)
+```
+
+**How it works:**
+1. Applies same filtering pipeline as TissueMask
+2. Identifies all connected tissue components
+3. Selects the largest connected component
+4. Returns bounding box encompassing that region
+
+**Best for:**
+- Slides with a single primary tissue section
+- Excluding small artifacts or tissue fragments
+- Focusing on main tissue area (default for most tilers)
+
+## Customizing Masks with Filters
+
+Masks accept custom filter chains for specialized tissue detection:
+
+```python
+from histolab.masks import TissueMask
+from histolab.filters.image_filters import RgbToGrayscale, OtsuThreshold
+from histolab.filters.morphological_filters import BinaryDilation, RemoveSmallHoles
+
+# Define custom filter composition
+custom_mask = TissueMask(
+    filters=[
+        RgbToGrayscale(),
+        OtsuThreshold(),
+        BinaryDilation(disk_size=5),
+        RemoveSmallHoles(area_threshold=500)
+    ]
+)
+```
+
+## Visualizing Masks
+
+### Using locate_mask()
+
+```python
+from histolab.slide import Slide
+from histolab.masks import TissueMask
+
+slide = Slide("slide.svs", processed_path="output/")
+mask = TissueMask()
+
+# Visualize mask boundaries on thumbnail
+slide.locate_mask(mask)
+```
+
+This displays the slide thumbnail with mask boundaries overlaid in a contrasting color.
+
+### Manual Visualization
+
+```python
+import matplotlib.pyplot as plt
+from histolab.masks import TissueMask
+
+slide = Slide("slide.svs", processed_path="output/")
+tissue_mask = TissueMask()
+
+# Generate mask
+mask_array = tissue_mask(slide)
+
+# Plot side by side
+fig, axes = plt.subplots(1, 2, figsize=(15, 7))
+
+axes[0].imshow(slide.thumbnail)
+axes[0].set_title("Original Slide")
+axes[0].axis('off')
+
+axes[1].imshow(mask_array, cmap='gray')
+axes[1].set_title("Tissue Mask")
+axes[1].axis('off')
+
+plt.show()
+```
+
+## Creating Custom Rectangular Masks
+
+Define specific regions of interest:
+
+```python
+from histolab.masks import BinaryMask
+import numpy as np
+
+class RectangularMask(BinaryMask):
+    def __init__(self, x_start, y_start, width, height):
+        self.x_start = x_start
+        self.y_start = y_start
+        self.width = width
+        self.height = height
+
+    def _mask(self, obj):
+        # Create mask with specified rectangular region
+        thumb = obj.thumbnail
+        mask = np.zeros(thumb.shape[:2], dtype=bool)
+        mask[self.y_start:self.y_start+self.height,
+             self.x_start:self.x_start+self.width] = True
+        return mask
+
+# Use custom mask
+roi_mask = RectangularMask(x_start=1000, y_start=500, width=2000, height=1500)
+```
+
+## Excluding Annotations
+
+Pathology slides often contain pen markings or digital annotations. Exclude them using custom masks:
+
+```python
+from histolab.masks import TissueMask
+from histolab.filters.image_filters import RgbToGrayscale, OtsuThreshold
+from histolab.filters.morphological_filters import BinaryDilation
+
+class AnnotationExclusionMask(BinaryMask):
+    def _mask(self, obj):
+        thumb = obj.thumbnail
+
+        # Convert to HSV to detect pen marks (often blue/green)
+        hsv = cv2.cvtColor(np.array(thumb), cv2.COLOR_RGB2HSV)
+
+        # Define color ranges for pen marks
+        lower_blue = np.array([100, 50, 50])
+        upper_blue = np.array([130, 255, 255])
+
+        # Create mask excluding pen marks
+        pen_mask = cv2.inRange(hsv, lower_blue, upper_blue)
+
+        # Apply standard tissue detection
+        tissue_mask = TissueMask()(obj)
+
+        # Combine: keep tissue, exclude pen marks
+        final_mask = tissue_mask & ~pen_mask.astype(bool)
+
+        return final_mask
+```
+
+## Integration with Tile Extraction
+
+Masks integrate seamlessly with tilers through the `extraction_mask` parameter:
+
+```python
+from histolab.tiler import RandomTiler
+from histolab.masks import TissueMask, BiggestTissueBoxMask
+
+# Use TissueMask to extract from all tissue
+random_tiler = RandomTiler(
+    tile_size=(512, 512),
+    n_tiles=100,
+    level=0,
+    extraction_mask=TissueMask()  # Extract from all tissue regions
+)
+
+# Or use default BiggestTissueBoxMask
+random_tiler = RandomTiler(
+    tile_size=(512, 512),
+    n_tiles=100,
+    level=0,
+    extraction_mask=BiggestTissueBoxMask()  # Default behavior
+)
+```
+
+## Best Practices
+
+1. **Preview masks before extraction**: Use `locate_mask()` or manual visualization to verify mask quality
+2. **Choose appropriate mask type**: Use `TissueMask` for multiple tissue sections, `BiggestTissueBoxMask` for single main sections
+3. **Customize for specific stains**: Different stains (H&E, IHC) may require adjusted threshold parameters
+4. **Handle artifacts**: Use custom filters or masks to exclude pen marks, bubbles, or folds
+5. **Test on diverse slides**: Validate mask performance across slides with varying quality and artifacts
+6. **Consider computational cost**: `TissueMask` is more comprehensive but computationally intensive than `BiggestTissueBoxMask`
+
+## Common Issues and Solutions
+
+### Issue: Mask includes too much background
+**Solution:** Adjust Otsu threshold or increase small object removal threshold
+
+### Issue: Mask excludes valid tissue
+**Solution:** Reduce small object removal threshold or modify dilation parameters
+
+### Issue: Multiple tissue sections, but only largest is captured
+**Solution:** Switch from `BiggestTissueBoxMask` to `TissueMask`
+
+### Issue: Pen annotations included in mask
+**Solution:** Implement custom annotation exclusion mask (see example above)

skills/histolab/references/visualization.md

@@ -0,0 +1,547 @@
+# Visualization
+
+## Overview
+
+Histolab provides several built-in visualization methods to help inspect slides, preview tile locations, visualize masks, and assess extraction quality. Proper visualization is essential for validating preprocessing pipelines, debugging extraction issues, and presenting results.
+
+## Slide Visualization
+
+### Thumbnail Display
+
+```python
+from histolab.slide import Slide
+import matplotlib.pyplot as plt
+
+slide = Slide("slide.svs", processed_path="output/")
+
+# Display thumbnail
+plt.figure(figsize=(10, 10))
+plt.imshow(slide.thumbnail)
+plt.title(f"Slide: {slide.name}")
+plt.axis('off')
+plt.show()
+```
+
+### Save Thumbnail to Disk
+
+```python
+# Save thumbnail as image file
+slide.save_thumbnail()
+# Saves to processed_path/thumbnails/slide_name_thumb.png
+```
+
+### Scaled Images
+
+```python
+# Get scaled version of slide at specific downsample factor
+scaled_img = slide.scaled_image(scale_factor=32)
+
+plt.imshow(scaled_img)
+plt.title(f"Slide at 32x downsample")
+plt.show()
+```
+
+## Mask Visualization
+
+### Using locate_mask()
+
+```python
+from histolab.masks import TissueMask, BiggestTissueBoxMask
+
+# Visualize TissueMask
+tissue_mask = TissueMask()
+slide.locate_mask(tissue_mask)
+
+# Visualize BiggestTissueBoxMask
+biggest_mask = BiggestTissueBoxMask()
+slide.locate_mask(biggest_mask)
+```
+
+This displays the slide thumbnail with mask boundaries overlaid in red.
+
+### Manual Mask Visualization
+
+```python
+import matplotlib.pyplot as plt
+from histolab.masks import TissueMask
+
+slide = Slide("slide.svs", processed_path="output/")
+mask = TissueMask()
+
+# Generate mask
+mask_array = mask(slide)
+
+# Create side-by-side comparison
+fig, axes = plt.subplots(1, 3, figsize=(20, 7))
+
+# Original thumbnail
+axes[0].imshow(slide.thumbnail)
+axes[0].set_title("Original Slide")
+axes[0].axis('off')
+
+# Binary mask
+axes[1].imshow(mask_array, cmap='gray')
+axes[1].set_title("Tissue Mask")
+axes[1].axis('off')
+
+# Overlay mask on thumbnail
+from matplotlib.colors import ListedColormap
+overlay = slide.thumbnail.copy()
+axes[2].imshow(overlay)
+axes[2].imshow(mask_array, cmap=ListedColormap(['none', 'red']), alpha=0.3)
+axes[2].set_title("Mask Overlay")
+axes[2].axis('off')
+
+plt.tight_layout()
+plt.show()
+```
+
+### Comparing Multiple Masks
+
+```python
+from histolab.masks import TissueMask, BiggestTissueBoxMask
+
+masks = {
+    'TissueMask': TissueMask(),
+    'BiggestTissueBoxMask': BiggestTissueBoxMask()
+}
+
+fig, axes = plt.subplots(1, len(masks) + 1, figsize=(20, 6))
+
+# Original
+axes[0].imshow(slide.thumbnail)
+axes[0].set_title("Original")
+axes[0].axis('off')
+
+# Each mask
+for idx, (name, mask) in enumerate(masks.items(), 1):
+    mask_array = mask(slide)
+    axes[idx].imshow(mask_array, cmap='gray')
+    axes[idx].set_title(name)
+    axes[idx].axis('off')
+
+plt.tight_layout()
+plt.show()
+```
+
+## Tile Location Preview
+
+### Using locate_tiles()
+
+Preview tile locations before extraction:
+
+```python
+from histolab.tiler import RandomTiler, GridTiler, ScoreTiler
+from histolab.scorer import NucleiScorer
+
+# RandomTiler preview
+random_tiler = RandomTiler(
+    tile_size=(512, 512),
+    n_tiles=50,
+    level=0,
+    seed=42
+)
+random_tiler.locate_tiles(slide, n_tiles=20)
+
+# GridTiler preview
+grid_tiler = GridTiler(
+    tile_size=(512, 512),
+    level=0
+)
+grid_tiler.locate_tiles(slide)
+
+# ScoreTiler preview
+score_tiler = ScoreTiler(
+    tile_size=(512, 512),
+    n_tiles=30,
+    scorer=NucleiScorer()
+)
+score_tiler.locate_tiles(slide, n_tiles=15)
+```
+
+This displays colored rectangles on the slide thumbnail indicating where tiles will be extracted.
+
+### Custom Tile Location Visualization
+
+```python
+import matplotlib.pyplot as plt
+import matplotlib.patches as patches
+from histolab.tiler import RandomTiler
+
+slide = Slide("slide.svs", processed_path="output/")
+tiler = RandomTiler(tile_size=(512, 512), n_tiles=30, seed=42)
+
+# Get thumbnail and scale factor
+thumbnail = slide.thumbnail
+scale_factor = slide.dimensions[0] / thumbnail.size[0]
+
+# Generate tile coordinates (without extracting)
+fig, ax = plt.subplots(figsize=(12, 12))
+ax.imshow(thumbnail)
+ax.set_title("Tile Locations Preview")
+ax.axis('off')
+
+# Manually add rectangles for each tile location
+# Note: This is conceptual - actual implementation would retrieve coordinates from tiler
+tile_coords = []  # Would be populated by tiler logic
+for coord in tile_coords:
+    x, y = coord[0] / scale_factor, coord[1] / scale_factor
+    w, h = 512 / scale_factor, 512 / scale_factor
+    rect = patches.Rectangle((x, y), w, h,
+                             linewidth=2, edgecolor='red',
+                             facecolor='none')
+    ax.add_patch(rect)
+
+plt.show()
+```
+
+## Tile Visualization
+
+### Display Extracted Tiles
+
+```python
+from pathlib import Path
+from PIL import Image
+import matplotlib.pyplot as plt
+
+tile_dir = Path("output/tiles/")
+tile_paths = list(tile_dir.glob("*.png"))[:16]  # First 16 tiles
+
+fig, axes = plt.subplots(4, 4, figsize=(12, 12))
+axes = axes.ravel()
+
+for idx, tile_path in enumerate(tile_paths):
+    tile_img = Image.open(tile_path)
+    axes[idx].imshow(tile_img)
+    axes[idx].set_title(tile_path.stem, fontsize=8)
+    axes[idx].axis('off')
+
+plt.tight_layout()
+plt.show()
+```
+
+### Tile Grid Mosaic
+
+```python
+def create_tile_mosaic(tile_dir, grid_size=(4, 4)):
+    """Create mosaic of tiles."""
+    tile_paths = list(Path(tile_dir).glob("*.png"))[:grid_size[0] * grid_size[1]]
+
+    fig, axes = plt.subplots(grid_size[0], grid_size[1], figsize=(16, 16))
+
+    for idx, tile_path in enumerate(tile_paths):
+        row = idx // grid_size[1]
+        col = idx % grid_size[1]
+        tile_img = Image.open(tile_path)
+        axes[row, col].imshow(tile_img)
+        axes[row, col].axis('off')
+
+    plt.tight_layout()
+    plt.savefig("tile_mosaic.png", dpi=150, bbox_inches='tight')
+    plt.show()
+
+create_tile_mosaic("output/tiles/", grid_size=(5, 5))
+```
+
+### Tile with Tissue Mask Overlay
+
+```python
+from histolab.tile import Tile
+import matplotlib.pyplot as plt
+
+# Assume we have a tile object
+tile = Tile(image=pil_image, coords=(x, y))
+
+# Calculate tissue mask
+tile.calculate_tissue_mask()
+
+fig, axes = plt.subplots(1, 3, figsize=(15, 5))
+
+# Original tile
+axes[0].imshow(tile.image)
+axes[0].set_title("Original Tile")
+axes[0].axis('off')
+
+# Tissue mask
+axes[1].imshow(tile.tissue_mask, cmap='gray')
+axes[1].set_title(f"Tissue Mask ({tile.tissue_ratio:.1%} tissue)")
+axes[1].axis('off')
+
+# Overlay
+axes[2].imshow(tile.image)
+axes[2].imshow(tile.tissue_mask, cmap='Reds', alpha=0.3)
+axes[2].set_title("Overlay")
+axes[2].axis('off')
+
+plt.tight_layout()
+plt.show()
+```
+
+## Quality Assessment Visualization
+
+### Tile Score Distribution
+
+```python
+import pandas as pd
+import matplotlib.pyplot as plt
+import seaborn as sns
+
+# Load tile report from ScoreTiler
+report_df = pd.read_csv("tiles_report.csv")
+
+# Score distribution histogram
+plt.figure(figsize=(10, 6))
+plt.hist(report_df['score'], bins=30, edgecolor='black', alpha=0.7)
+plt.xlabel('Tile Score')
+plt.ylabel('Frequency')
+plt.title('Distribution of Tile Scores')
+plt.grid(axis='y', alpha=0.3)
+plt.show()
+
+# Score vs tissue percentage scatter
+plt.figure(figsize=(10, 6))
+plt.scatter(report_df['tissue_percent'], report_df['score'], alpha=0.5)
+plt.xlabel('Tissue Percentage')
+plt.ylabel('Tile Score')
+plt.title('Tile Score vs Tissue Coverage')
+plt.grid(alpha=0.3)
+plt.show()
+```
+
+### Top vs Bottom Scoring Tiles
+
+```python
+import pandas as pd
+from PIL import Image
+import matplotlib.pyplot as plt
+
+# Load tile report
+report_df = pd.read_csv("tiles_report.csv")
+report_df = report_df.sort_values('score', ascending=False)
+
+# Top 8 tiles
+top_tiles = report_df.head(8)
+# Bottom 8 tiles
+bottom_tiles = report_df.tail(8)
+
+fig, axes = plt.subplots(2, 8, figsize=(20, 6))
+
+# Display top tiles
+for idx, (_, row) in enumerate(top_tiles.iterrows()):
+    tile_img = Image.open(f"output/tiles/{row['tile_name']}")
+    axes[0, idx].imshow(tile_img)
+    axes[0, idx].set_title(f"Score: {row['score']:.3f}", fontsize=8)
+    axes[0, idx].axis('off')
+
+# Display bottom tiles
+for idx, (_, row) in enumerate(bottom_tiles.iterrows()):
+    tile_img = Image.open(f"output/tiles/{row['tile_name']}")
+    axes[1, idx].imshow(tile_img)
+    axes[1, idx].set_title(f"Score: {row['score']:.3f}", fontsize=8)
+    axes[1, idx].axis('off')
+
+axes[0, 0].set_ylabel('Top Scoring', fontsize=12)
+axes[1, 0].set_ylabel('Bottom Scoring', fontsize=12)
+
+plt.tight_layout()
+plt.savefig("score_comparison.png", dpi=150, bbox_inches='tight')
+plt.show()
+```
+
+## Multi-Slide Visualization
+
+### Slide Collection Thumbnails
+
+```python
+from pathlib import Path
+from histolab.slide import Slide
+import matplotlib.pyplot as plt
+
+slide_dir = Path("slides/")
+slide_paths = list(slide_dir.glob("*.svs"))[:9]
+
+fig, axes = plt.subplots(3, 3, figsize=(15, 15))
+axes = axes.ravel()
+
+for idx, slide_path in enumerate(slide_paths):
+    slide = Slide(slide_path, processed_path="output/")
+    axes[idx].imshow(slide.thumbnail)
+    axes[idx].set_title(slide.name, fontsize=10)
+    axes[idx].axis('off')
+
+plt.tight_layout()
+plt.savefig("slide_collection.png", dpi=150, bbox_inches='tight')
+plt.show()
+```
+
+### Tissue Coverage Comparison
+
+```python
+from pathlib import Path
+from histolab.slide import Slide
+from histolab.masks import TissueMask
+import matplotlib.pyplot as plt
+import numpy as np
+
+slide_paths = list(Path("slides/").glob("*.svs"))
+tissue_percentages = []
+slide_names = []
+
+for slide_path in slide_paths:
+    slide = Slide(slide_path, processed_path="output/")
+    mask = TissueMask()(slide)
+    tissue_pct = mask.sum() / mask.size * 100
+    tissue_percentages.append(tissue_pct)
+    slide_names.append(slide.name)
+
+# Bar plot
+plt.figure(figsize=(12, 6))
+plt.bar(range(len(slide_names)), tissue_percentages)
+plt.xticks(range(len(slide_names)), slide_names, rotation=45, ha='right')
+plt.ylabel('Tissue Coverage (%)')
+plt.title('Tissue Coverage Across Slides')
+plt.grid(axis='y', alpha=0.3)
+plt.tight_layout()
+plt.show()
+```
+
+## Filter Effect Visualization
+
+### Before and After Filtering
+
+```python
+from histolab.filters.image_filters import RgbToGrayscale, HistogramEqualization
+from histolab.filters.compositions import Compose
+
+# Define filter pipeline
+filter_pipeline = Compose([
+    RgbToGrayscale(),
+    HistogramEqualization()
+])
+
+# Original vs filtered
+fig, axes = plt.subplots(1, 2, figsize=(12, 6))
+
+axes[0].imshow(slide.thumbnail)
+axes[0].set_title("Original")
+axes[0].axis('off')
+
+filtered = filter_pipeline(slide.thumbnail)
+axes[1].imshow(filtered, cmap='gray')
+axes[1].set_title("After Filtering")
+axes[1].axis('off')
+
+plt.tight_layout()
+plt.show()
+```
+
+### Multi-Step Filter Visualization
+
+```python
+from histolab.filters.image_filters import RgbToGrayscale, OtsuThreshold
+from histolab.filters.morphological_filters import BinaryDilation, RemoveSmallObjects
+
+# Individual filter steps
+steps = [
+    ("Original", None),
+    ("Grayscale", RgbToGrayscale()),
+    ("Otsu Threshold", Compose([RgbToGrayscale(), OtsuThreshold()])),
+    ("After Dilation", Compose([RgbToGrayscale(), OtsuThreshold(), BinaryDilation(disk_size=5)])),
+    ("Remove Small Objects", Compose([RgbToGrayscale(), OtsuThreshold(), BinaryDilation(disk_size=5), RemoveSmallObjects(area_threshold=500)]))
+]
+
+fig, axes = plt.subplots(1, len(steps), figsize=(20, 4))
+
+for idx, (title, filter_fn) in enumerate(steps):
+    if filter_fn is None:
+        axes[idx].imshow(slide.thumbnail)
+    else:
+        result = filter_fn(slide.thumbnail)
+        axes[idx].imshow(result, cmap='gray')
+    axes[idx].set_title(title, fontsize=10)
+    axes[idx].axis('off')
+
+plt.tight_layout()
+plt.show()
+```
+
+## Exporting Visualizations
+
+### High-Resolution Exports
+
+```python
+# Export high-resolution figure
+fig, ax = plt.subplots(figsize=(20, 20))
+ax.imshow(slide.thumbnail)
+ax.axis('off')
+plt.savefig("slide_high_res.png", dpi=300, bbox_inches='tight', pad_inches=0)
+plt.close()
+```
+
+### PDF Reports
+
+```python
+from matplotlib.backends.backend_pdf import PdfPages
+
+# Create multi-page PDF report
+with PdfPages('slide_report.pdf') as pdf:
+    # Page 1: Slide thumbnail
+    fig1, ax1 = plt.subplots(figsize=(10, 10))
+    ax1.imshow(slide.thumbnail)
+    ax1.set_title(f"Slide: {slide.name}")
+    ax1.axis('off')
+    pdf.savefig(fig1, bbox_inches='tight')
+    plt.close()
+
+    # Page 2: Tissue mask
+    fig2, ax2 = plt.subplots(figsize=(10, 10))
+    mask = TissueMask()(slide)
+    ax2.imshow(mask, cmap='gray')
+    ax2.set_title("Tissue Mask")
+    ax2.axis('off')
+    pdf.savefig(fig2, bbox_inches='tight')
+    plt.close()
+
+    # Page 3: Tile locations
+    fig3, ax3 = plt.subplots(figsize=(10, 10))
+    tiler = RandomTiler(tile_size=(512, 512), n_tiles=30)
+    tiler.locate_tiles(slide)
+    pdf.savefig(fig3, bbox_inches='tight')
+    plt.close()
+```
+
+## Interactive Visualization (Jupyter)
+
+### IPython Widgets for Exploration
+
+```python
+from ipywidgets import interact, IntSlider
+import matplotlib.pyplot as plt
+from histolab.filters.morphological_filters import BinaryDilation
+
+@interact(disk_size=IntSlider(min=1, max=20, value=5))
+def explore_dilation(disk_size):
+    """Interactive dilation exploration."""
+    filter_pipeline = Compose([
+        RgbToGrayscale(),
+        OtsuThreshold(),
+        BinaryDilation(disk_size=disk_size)
+    ])
+    result = filter_pipeline(slide.thumbnail)
+
+    plt.figure(figsize=(10, 10))
+    plt.imshow(result, cmap='gray')
+    plt.title(f"Binary Dilation (disk_size={disk_size})")
+    plt.axis('off')
+    plt.show()
+```
+
+## Best Practices
+
+1. **Always preview before processing**: Use thumbnails and `locate_tiles()` to validate settings
+2. **Use side-by-side comparisons**: Show before/after for filter effects
+3. **Label clearly**: Include titles, axes labels, and legends
+4. **Export high-resolution**: Use 300 DPI for publication-quality figures
+5. **Save intermediate visualizations**: Document processing steps
+6. **Use colormaps appropriately**: 'gray' for binary masks, 'viridis' for heatmaps
+7. **Create reusable visualization functions**: Standardize reporting across projects