Whole-slide imaging

pydcm.wsi reads DICOM WSI pyramids with a tile/region API — open a slide (one file or a multi-file pyramid), inspect levels, and read regions or tiles. Validated bit-exact against reference decodes on multi-vendor WSI.

Open and inspect

from pydcm import wsi

slide = wsi.open_slide("wsi_dir/")     # a directory or a single instance
slide.level_count                       # number of pyramid levels
slide.level_dimensions                  # [(w0, h0), (w1, h1), …] per level
slide.properties                        # vendor / objective-power / MPP metadata

Read a region

region = slide.read_region((x, y), level=0, size=(512, 512))   # RGBA ndarray
rgb    = slide.read_region((x, y), level=0, size=(512, 512), rgba=False)

read_region uses level-0 reference coordinates: location is in level-0 reference coordinates, size is in the target level's pixels.

Thumbnails and associated images

thumb = slide.get_thumbnail((1024, 1024))      # RGB ndarray
label = slide.associated_images["LABEL"]       # LABEL / OVERVIEW / THUMBNAIL

Tiles for a viewer

For a tiled viewer or a tile-streaming pipeline, the level/tile grid is exposed directly so you can fetch tiles without decoding a whole region:

tile = slide.read_tile(level=0, tile=(3, 7))   # a single decoded tile (col, row)
desc = slide.viewer_level(0)                     # level metadata + tile range grid

ICC handling is available where the slide carries a profile: slide.icc_profile gives the raw profile, and read_associated_image(..., apply_icc_profile=True) and get_total_pixel_matrix(..., apply_icc_profile=True) apply it.