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

uv pip install histolab

Quick Start

Basic workflow for extracting tiles from a whole slide image:

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:

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:

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:

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:

# 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:

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:

how to use histolab
CursorClaude CodeClineCodexWindsurfGooseGitHub CopilotVS CodeGemini CLIKiloOpencodeKimi CLIRoo ClineAiderContinueZedBolt.newLovablev0Replit AgentSweepSmol DeveloperDevinCavemanAmpAntigravity
How to use histolab on Cursor
AI-first code editor with Composer
1
Prerequisites
Before installing skills in Cursor, ensure your development environment meets these requirements:
›Cursor installed and configured on your development machine
›Node.js version 16.0+ with npm package manager (verify with node --version)
›Active project directory or workspace where you want to add histolab
2
Execute installation command
Execute the skills CLI command in your project's root directory to begin installation:
$npx skills add https://github.com/davila7/claude-code-templates --skill histolabcopy
The skills CLI fetches histolab from GitHub repository davila7/claude-code-templates and configures it for Cursor.
3
Select Cursor when prompted
The CLI will show a list of available agents. Use arrow keys to navigate and space to select Cursor:
◆ Which agents do you want to install to?
│
│ ── Universal (.agents/skills) ── always included ────
│   • Amp
│   • Antigravity
│   • Cline
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│ ●Cursor(selected)
│   • Cursor
│   • Windsurf
4
Verify installation
Confirm successful installation by checking the skill directory location:
.cursor/skills/histolab
Reload or restart Cursor to activate histolab. Access the skill through slash commands (e.g., /histolab) or your agent's skill management interface.
⚠
Security & Verification Notice
We perform automated surface-level scans (Gen AI Scanner, Socket, Snyk) during installation. These checks detect common vulnerabilities but do not guarantee complete security. Always review skill source code and verify the publisher's reputation before production use.
Skills execute code in your development environment. Always verify the publisher's identity, review recent commits, and test in isolated environments before production deployment.
Additional Resources
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