Crate slideforge 

Fast whole slide image (WSI) tile extraction, with tissue detection and stain normalization.

Whole slide images are gigapixel-scale microscopy scans used in digital pathology, stored as tiled, pyramidal (multi-resolution) TIFF files. Slideforge currently reads the Aperio SVS format.

Slide opens a single WSI and extracts tiles at a specific pyramid level or a target microns-per-pixel value, optionally dropping background-only tiles (Otsu thresholding) and normalizing stain color (Reinhard normalization) along the way. Extracted tiles can be written out as loose JPEGs, a .tfrecord file for ML training pipelines, and/or summarized in a PDF report. Dataset extends this across a whole directory of slides at once.

Example

use slideforge::slide::{Slide, SlideOutputs};
use slideforge::ExtractionOptions;

let slide = Slide::open("slide.svs")?;

let options = ExtractionOptions::parallel()
    .with_target_mpp(0.5)
    .with_min_tissue_fraction(0.1)
    .with_stain_normalization();

let outputs = SlideOutputs::default().with_tile_dir("tiles/");

slide.extract(&options, &outputs, |tile| {
    println!("kept tile ({}, {})", tile.tile_x(), tile.tile_y());
    Ok(())
})?;

Re-exports

pub use extraction::ExtractionOptions;

pub use extraction::Parallelism;

pub use filter::TissueMask;

pub use logging::ExtractionObserver;

pub use logging::ExtractionStats;

pub use logging::ProgressBar;

pub use logging::ReportCollector;

pub use logging::SimpleLogging;

pub use metadata::Dimensions;

pub use metadata::Level;

pub use metadata::Metadata;

pub use metadata::TileSize;

pub use report::ExtractionReport;

pub use stain::normalize_reinhard;

Modules

backend

Vendor-specific WSI format parsers. Currently just Aperio SVS.

dataset

Batch tile extraction across a directory of slides.

decoder

Tile image decoding. Currently just JPEG, via JpegDecoder.

error

The crate’s single error type, WsiError.

extraction

Extraction options controlling how tiles are decoded and processed during extraction.

filter

Basic tissue filtering methods for tiles

logging

Modular logging/observability utilities.

metadata

Vendor-independent metadata representations for Whole Slide Images (WSIs).

report

Extraction report generation.

slide

Whole slide image (WSI) reading and tile extraction.

stain

Reinhard color/stain normalization for RGB tile images.

tfrecord

Writes tile records to the .tfrecord format used by TensorFlow

tile

Tile directory and tile reading functionality for tiled TIFF images.