statumen

Overview

statumen is a Signinum-native WSI reader. It owns container parsing, slide/scene/level/plane geometry, and the SlideReader trait. Codec work is delegated to the signinum-* crates.

Architecture

• Container parsers: TIFF/SVS/NDPI/DICOM/Zeiss/Mirax/Hamamatsu/Philips TIFF.
• Slide geometry: Slide, Dataset, SceneId, LevelIdx, PlaneIdx.
• Signinum integration: compressed tile resolution feeds signinum_jpeg and signinum_j2k.
• DICOM is the unified reader for the workspace; sv-slide routes .dcm through the same statumen adapter as other WSI formats.
• Parity oracle: vendored jpeg-decoder and dynamically loaded compatibility library paths are test-only.

DICOM

The DICOM reader supports VL Whole Slide Microscopy pyramids assembled from a single file or sibling instances in the same series. Phase 7a coverage includes JPEG baseline where signinum supports the JPEG bitstream, JPEG 2000, RLE Lossless for 8-bit RGB/monochrome frames, native uncompressed Explicit VR Little Endian, Implicit VR Little Endian, Explicit VR Big Endian for 8-bit frames, row-major multi-frame tile addressing, associated image discovery, and sparse tiled frame maps.

Quick Start

use std::path::Path;
use statumen::{PlaneSelection, Slide, TileOutputPreference, TilePixels, TileRequest};

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let slide = Slide::open(Path::new("sample.svs"))?;
    let req = TileRequest {
        scene: 0,
        series: 0,
        level: 0,
        plane: PlaneSelection::default(),
        col: 0,
        row: 0,
    };

    let tile = slide.read_tile(&req, TileOutputPreference::cpu())?;
    if let TilePixels::Cpu(cpu) = tile {
        println!("decoded {}x{} tile", cpu.width, cpu.height);
    }
    Ok(())
}

Performance

Benchmark notes and phase reports are maintained in the project repository.

Optional Iris comparison is wired through scripts/iris_bench.py and the existing bench_driver workloads. Iris consumes pre-encoded .iris slides, so set WSI_BENCH_INCLUDE_IRIS=1 plus either WSI_IRIS_SLIDE_PATH=/path/file.iris for a single slide or WSI_IRIS_SLIDE_DIR=/path/to/iris-slides for a directory containing <source-stem>.iris files. Set WSI_BENCH_GATE_IRIS=1 only when the run should fail if statumen is slower than Iris.

Codec Library

All production JPEG and JPEG 2000 decode is delegated to the sibling signinum repository. Cite signinum's JOSS paper for codec methods, ROI/restart-marker APIs, batch decode, and decode-performance claims.

For reader behavior, container parsing, and SlideViewer integration, cite this workspace separately until a reader-specific artifact exists.

License

Apache-2.0. See the sibling signinum repo for codec implementation details and its own license metadata.