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name: "histolab-wsi-processing" description: "WSI processing for digital pathology. Tissue detection, tile extraction (random, grid, score-based), filter pipelines for H&E/IHC. For dataset prep, tile-based DL, slide QC. Use pathml for multiplexed imaging." license: Apache-2.0

Histolab WSI Processing

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 using multiple strategies, and provides composable filter pipelines for preprocessing. The library handles SVS, TIFF, NDPI, and other WSI formats via OpenSlide.

When to Use

• Extracting tiles from whole slide images for deep learning model training
• Detecting tissue regions and filtering background/artifacts in histopathology slides
• Building preprocessing pipelines for H&E or IHC stained tissue sections
• Creating quality-driven tile datasets ranked by nuclei density or cellularity
• Performing batch tile extraction across slide collections with consistent parameters
• Assessing slide quality and tissue coverage before computational pathology workflows
• For raw slide access without tile extraction, use openslide-python directly
• For complex multiplexed imaging or spatial proteomics pipelines, use pathml instead

Prerequisites

• Python packages: histolab (includes OpenSlide Python bindings)
• System dependency: OpenSlide C library must be installed separately
• Supported formats: SVS, TIFF, NDPI, VMS, SCN, MRXS (via OpenSlide)

# macOS
brew install openslide
pip install histolab

# Ubuntu/Debian
sudo apt-get install openslide-tools
pip install histolab

Quick Start

from histolab.slide import Slide
from histolab.tiler import RandomTiler

# Load slide
slide = Slide("slide.svs", processed_path="output/")
print(f"Dimensions: {slide.dimensions}, Levels: {slide.levels}")

# Configure tiler
tiler = RandomTiler(
    tile_size=(512, 512), n_tiles=100, level=0, seed=42,
    check_tissue=True, tissue_percent=80.0
)

# Preview and extract
tiler.locate_tiles(slide, n_tiles=20)
tiler.extract(slide)

Core API

Module 1: Slide Management

The Slide class is the primary interface for loading and inspecting WSI files.

from histolab.slide import Slide
from histolab.data import prostate_tissue

# Load from built-in sample data (prostate, ovarian, breast, heart, kidney)
prostate_svs, prostate_path = prostate_tissue()
slide = Slide(prostate_path, processed_path="output/")

# Inspect properties
print(f"Dimensions: {slide.dimensions}")       # (width, height) at level 0
print(f"Levels: {slide.levels}")               # Number of pyramid levels
print(f"Level dims: {slide.level_dimensions}") # Dimensions per level
print(f"Magnification: {slide.properties.get('openslide.objective-power', 'N/A')}")
print(f"MPP-X: {slide.properties.get('openslide.mpp-x', 'N/A')}")

# Thumbnail and scaled image
slide.save_thumbnail()  # Saves to processed_path
scaled = slide.scaled_image(scale_factor=32)

# Extract region at specific coordinates
region = slide.extract_region(location=(1000, 2000), size=(512, 512), level=0)

Module 2: Tissue Detection

Mask classes identify tissue regions and filter background for tile extraction.

from histolab.masks import TissueMask, BiggestTissueBoxMask, BinaryMask
import numpy as np

# TissueMask: segments ALL tissue regions (multiple sections)
tissue_mask = TissueMask()
mask_array = tissue_mask(slide)  # Binary NumPy array: True=tissue, False=background
print(f"Tissue coverage: {mask_array.sum() / mask_array.size * 100:.1f}%")

# BiggestTissueBoxMask: bounding box of largest tissue region (default)
biggest_mask = BiggestTissueBoxMask()

# Visualize mask on slide thumbnail
slide.locate_mask(tissue_mask)

# Custom mask via BinaryMask subclass
class RectangularROI(BinaryMask):
    def __init__(self, x, y, w, h):
        self.x, self.y, self.w, self.h = x, y, w, h

    def _mask(self, slide):
        thumb = slide.thumbnail
        mask = np.zeros(thumb.shape[:2], dtype=bool)
        mask[self.y:self.y+self.h, self.x:self.x+self.w] = True
        return mask

Module 3: Tile Extraction

Three strategies for extracting tiles: random sampling, grid coverage, and score-based selection.

from histolab.tiler import RandomTiler, GridTiler, ScoreTiler
from histolab.scorer import NucleiScorer
from histolab.masks import TissueMask

# RandomTiler: fixed number of randomly positioned tiles
random_tiler = RandomTiler(
    tile_size=(512, 512), n_tiles=100, level=0,
    seed=42, check_tissue=True, tissue_percent=80.0
)
random_tiler.locate_tiles(slide, n_tiles=20)  # Preview first
random_tiler.extract(slide)

# GridTiler: systematic grid coverage
grid_tiler = GridTiler(
    tile_size=(512, 512), level=0,
    pixel_overlap=0, check_tissue=True, tissue_percent=70.0
)
grid_tiler.extract(slide, extraction_mask=TissueMask())

# ScoreTiler: top-ranked tiles by scoring function
score_tiler = ScoreTiler(
    tile_size=(512, 512), n_tiles=50, level=0,
    scorer=NucleiScorer(), check_tissue=True
)
score_tiler.extract(slide, report_path="tiles_report.csv")
# Report CSV: tile_name, x_coord, y_coord, level, score, tissue_percent

Module 4: Filters and Preprocessing

Composable image and morphological filters for tissue detection and preprocessing.

from histolab.filters.image_filters import (
    RgbToGrayscale, RgbToHsv, RgbToHed,
    OtsuThreshold, AdaptiveThreshold,
    StretchContrast, HistogramEqualization, Invert
)
from histolab.filters.morphological_filters import (
    BinaryDilation, BinaryErosion, BinaryOpening, BinaryClosing,
    RemoveSmallObjects, RemoveSmallHoles
)
from histolab.filters.compositions import Compose

# Standard tissue detection pipeline
tissue_pipeline = Compose([
    RgbToGrayscale(),
    OtsuThreshold(),
    BinaryDilation(disk_size=5),
    RemoveSmallHoles(area_threshold=1000),
    RemoveSmallObjects(area_threshold=500)
])

# Use custom pipeline with TissueMask
from histolab.masks import TissueMask
custom_mask = TissueMask(filters=tissue_pipeline)

# Stain deconvolution (H&E)
hed_filter = RgbToHed()  # Hematoxylin-Eosin-DAB separation

# Apply filters to individual tiles
from histolab.tile import Tile

filter_chain = Compose([RgbToGrayscale(), StretchContrast()])
filtered_tile = tile.apply_filters(filter_chain)

# Lambda for custom inline filters
from histolab.filters.image_filters import Lambda
import numpy as np

brightness = Lambda(lambda img: np.clip(img * 1.2, 0, 255).astype(np.uint8))
red_channel = Lambda(lambda img: img[:, :, 0])

Module 5: Scoring

Scorers rank tiles by tissue content quality for use with ScoreTiler.

from histolab.scorer import NucleiScorer, CellularityScorer, Scorer
import numpy as np

# Built-in scorers
nuclei = NucleiScorer()       # Scores by nuclei density (grayscale threshold + count)
cellularity = CellularityScorer()  # Scores by overall cellular content

# Custom scorer
class ColorVarianceScorer(Scorer):
    def __call__(self, tile):
        """Score tiles by color variance (higher = more informative)."""
        tile_array = np.array(tile.image)
        return np.var(tile_array, axis=(0, 1)).sum()

score_tiler = ScoreTiler(
    tile_size=(512, 512), n_tiles=30,
    scorer=ColorVarianceScorer()
)

Module 6: Visualization

Built-in methods and matplotlib patterns for inspecting slides, masks, and tiles.

import matplotlib.pyplot as plt
from histolab.masks import TissueMask

# Built-in: mask overlay on slide thumbnail
slide.locate_mask(TissueMask())

# Built-in: tile location preview
tiler.locate_tiles(slide, n_tiles=20)

# Manual side-by-side: slide vs mask
mask = TissueMask()
mask_array = mask(slide)
fig, axes = plt.subplots(1, 2, figsize=(15, 7))
axes[0].imshow(slide.thumbnail); axes[0].set_title("Slide"); axes[0].axis('off')
axes[1].imshow(mask_array, cmap='gray'); axes[1].set_title("Mask"); axes[1].axis('off')
plt.tight_layout()
plt.show()

# 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))
for idx, tp in enumerate(axes.ravel()):
    if idx < len(tile_paths):
        tp.imshow(Image.open(tile_paths[idx]))
        tp.set_title(tile_paths[idx].stem, fontsize=8)
    tp.axis('off')
plt.tight_layout()
plt.show()

Key Concepts

WSI Pyramid Levels

Whole slide images use a pyramidal structure with multiple resolution levels. Level 0 is the highest resolution (native scan). Higher levels provide progressively lower resolutions for faster access.

for level in range(slide.levels):
    dims = slide.level_dimensions[level]
    downsample = slide.level_downsamples[level]
    print(f"Level {level}: {dims}, downsample: {downsample:.0f}x")
# Level 0: (98304, 221184), downsample: 1x
# Level 1: (24576, 55296), downsample: 4x

Filter Composition Pattern

Filters are designed to be chained via Compose. The output of one filter becomes the input of the next. Image filters operate on RGB/grayscale arrays; morphological filters operate on binary arrays. Order matters: always convert to the expected input type before applying downstream filters.

Mask-Tiler Integration

All tilers accept an extraction_mask parameter. The default is BiggestTissueBoxMask(). Override with TissueMask() for multi-section slides or a custom BinaryMask subclass for ROI-specific extraction.

Common Workflows

Workflow 1: Exploratory Slide Analysis

Goal: Quickly inspect a slide, detect tissue, and sample diverse regions for review.

from histolab.slide import Slide
from histolab.tiler import RandomTiler
from histolab.masks import TissueMask
import matplotlib.pyplot as plt
import logging

logging.basicConfig(level=logging.INFO)

slide = Slide("slide.svs", processed_path="output/exploratory/")
print(f"Dimensions: {slide.dimensions}, Levels: {slide.levels}")
slide.save_thumbnail()

# Visualize tissue detection
tissue_mask = TissueMask()
slide.locate_mask(tissue_mask)
mask_arr = tissue_mask(slide)
print(f"Tissue coverage: {mask_arr.sum() / mask_arr.size * 100:.1f}%")

# Sample tiles
tiler = RandomTiler(
    tile_size=(512, 512), n_tiles=50, level=0,
    seed=42, check_tissue=True, tissue_percent=80.0
)
tiler.locate_tiles(slide, n_tiles=20)
tiler.extract(slide)

Workflow 2: Deep Learning Dataset Preparation

Goal: Build a quality-controlled tile dataset from multiple slides for model training.

from pathlib import Path
from histolab.slide import Slide
from histolab.tiler import ScoreTiler
from histolab.scorer import NucleiScorer
import pandas as pd
import logging

logging.basicConfig(level=logging.INFO)

slide_dir = Path("slides/")
output_base = Path("output/dataset/")
all_reports = []

tiler = ScoreTiler(
    tile_size=(512, 512), n_tiles=100, level=0,
    scorer=NucleiScorer(), check_tissue=True, tissue_percent=80.0
)

for slide_path in sorted(slide_dir.glob("*.svs")):
    out_dir = output_base / slide_path.stem
    out_dir.mkdir(parents=True, exist_ok=True)
    slide = Slide(str(slide_path), processed_path=str(out_dir))
    slide.save_thumbnail()
    report_path = str(out_dir / "report.csv")
    tiler.extract(slide, report_path=report_path)
    df = pd.read_csv(report_path)
    df["slide"] = slide_path.stem
    all_reports.append(df)
    print(f"{slide_path.stem}: {len(df)} tiles, mean score {df['score'].mean():.3f}")

combined = pd.concat(all_reports, ignore_index=True)
combined.to_csv(output_base / "dataset_manifest.csv", index=False)
print(f"Total: {len(combined)} tiles from {len(all_reports)} slides")

Workflow 3: Custom Tissue Detection with Artifact Removal

Goal: Handle slides with pen annotations or unusual staining using custom filter pipelines.

from histolab.slide impo