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Inspect Slides And Preview Tiles

Overview

Problem solved: verify that a slide opens correctly, confirm the working resolution you want, and save a few preview regions before you launch a larger tiling job.

Use this example when:

  • you are onboarding a new slide source,
  • you want to sanity-check mpp or level choice visually,
  • or you need to confirm that tiles, masks, or annotations will line up at the expected scale.

Why This Approach

OpenSlide gives you direct access to slide pyramid metadata and patch reads. This is the simplest way to inspect a single slide before you commit to a distributed Ray pipeline.

Bundled example input

The figure below shows the intended inspection workflow: a slide thumbnail for context, one larger preview region, and one saved tile for close inspection.

Slide inspection preview from the bundled demo slide The slide thumbnail marks one larger preview region in red and one saved tile in blue.

Example

from pathlib import Path

from PIL import Image

from ratiopath.openslide import OpenSlide

output_dir = Path("preview")
output_dir.mkdir(exist_ok=True)

with OpenSlide("slide.svs") as slide:
    level = slide.closest_level(0.5)
    resolution = slide.slide_resolution(level)
    extent = slide.level_dimensions[level]

    print(f"Selected level: {level}")
    print(f"Resolution: {resolution}")
    print(f"Extent: {extent}")

    region = slide.read_region_relative(
        location=(0, 0),
        level=level,
        size=(2048, 2048),
    ).convert("RGB")
    region.save(output_dir / "region_preview.png")

    tile = slide.read_tile(
        x=1024,
        y=1024,
        extent_x=512,
        extent_y=512,
        level=level,
    )
    Image.fromarray(tile).save(output_dir / "tile_preview.png")
Example output 
Selected level: 2
Resolution: (0.5, 0.5)
Extent: (16384, 12288)
Under the hood

closest_level compares your target physical resolution with the available pyramid levels and picks the nearest one. read_region_relative and read_tile then interpret coordinates in that chosen level's coordinate system.

This is important for debugging because it lets you reason in the same working space that later tiling code will use. If a preview looks wrong here, the larger distributed pipeline will be wrong too.

What To Check

  • whether the selected level matches the physical scale you expect,
  • whether bright background and tissue look sensible at that scale,
  • whether the saved tile boundaries correspond to the intended region,
  • and whether any overlay or annotation source uses the same slide orientation.