Digital pathology primer

Digital pathology primer#

Digital pathology turns a glass tissue slide into a whole-slide image (WSI). A WSI can contain billions of pixels, so analysis usually happens at several resolutions and on many smaller image regions.

The minimum vocabulary#

Pyramid level : A WSI stores the same scene at multiple resolutions. Level 0 is normally the highest resolution; larger level numbers are progressively downsampled.

Microns per pixel (MPP) : The physical size represented by one pixel. A smaller MPP means higher resolution. Approximately 0.5 MPP is commonly associated with 20× scanning and 0.25 MPP with 40×, but scanner metadata should be preferred over this approximation.

Tissue segmentation : Separating tissue from the glass background. The result is usually one or more polygons rather than a new cropped image.

Tile or patch : A small rectangular image sampled from the WSI. LazySlide records tile coordinates first and reads their pixels only when an operation needs them.

Feature embedding : A numerical vector describing the appearance of a tile. It can be used for visualization, clustering, prediction, or slide-level aggregation.

Annotation : A point, line, or polygon associated with a region of the slide, often created by a pathologist or another image-analysis tool.

A typical analysis#

slide file -> inspect metadata -> find tissue -> create tiles
           -> quality control -> extract features -> analyze or predict
           -> visualize -> save

LazySlide stores the source image, spatial shapes, feature tables, and metadata in a WSIData object. Most operations add a result to that object instead of returning a disconnected array. See How LazySlide stores results before building a longer pipeline.

Three resolution decisions#

Do not treat pyramid level, magnification, and MPP as interchangeable knobs:

  • Use MPP when an algorithm or model expects a physical resolution.

  • Use a pyramid level when directly inspecting or segmenting a particular stored level.

  • Use tile size in pixels together with MPP to define the physical field of view.

For example, a 256-pixel tile at 0.5 MPP covers 128 microns in each direction. The same tile at 0.25 MPP covers 64 microns.

Next, analyze your first slide.