wsi-rs 0.9.0

wsi-rs 0.9.0 uses J2K 0.13.1 and JXR 0.4.0, and needs Rust 1.99 or newer. The previous crates.io release was 0.8.0. This release also includes the changes listed under 0.8.1 in the changelog.

The Python bindings are now on PyPI as wsi-rs, so pip install wsi-rs works. Its abi3 wheels support Python 3.10 and newer on:

• Linux x86_64 and aarch64;
• macOS arm64 and x86_64;
• Windows x64.

The wheels and sdist are attached to this release.

[0.9.0] - 2026-10-29

Added

• Opens TIFFs stored in strips when the largest image is 8-bit grayscale or
  RGB, uncompressed or compressed with LZW, Deflate, Zstd or JPEG, including
  YCbCr JPEG and the horizontal predictor. Before, only a single-image
  uncompressed 8-bit RGB TIFF opened. A tile read decodes only the strips it
  covers, so images over the 128 MiB decoded-image limit open; each compressed
  strip must fit it. Other images in the file become associated images.
  16-bit, palette, CMYK and alpha strip images still return an error, and a
  strip-only .vsi file without its companion folder is not opened as a
  plain TIFF.
• Slide::tile_location and Slide::level_tile_locations report where tiles'
  encoded bytes are stored: the file, byte ranges, framing (Standalone,
  JpegTables, BarePayload or Prefixed) and the codec parameters a decoder
  outside wsi-rs needs, or that a tile is Absent or NotAddressable and why.
  EncodedUnit::assemble turns the bytes at those ranges into a standalone
  stream; for a unit that covers its whole tile it equals what
  read_raw_compressed_tile returns, except for bare payloads that raw reads
  return as reordered or decoded samples. A unit a tile is cut from assembles
  to the whole stored image. Every range is checked against the file size,
  and a level listing stays within the tile-index limit. Every slide format
  reports locations; .svcache files, which hold wsi-rs's own decoded tiles,
  do not. (#27)
• read_raw_compressed_tile covers tiles it used to reject. A tile cut from a
  larger stored JPEG (Ventana subtiles, NDPI levels without restart markers,
  MIRAX and CZI crops, strip-based TIFFs, ZVI windows) is cropped in the
  coefficient domain, as jpegtran -crop does: quantized coefficients are kept
  and only the entropy coding is redone. When the tile origin is not on the
  JPEG's MCU grid, the crop starts at the previous MCU boundary and the new
  RawCompressedTile::tile_region locates the tile. A crop holds the whole
  source unit's DCT coefficients, about 12 bytes per pixel for a 4:4:4 JPEG,
  and its working set must fit the new SlideLimits::lossless_crop_bytes
  (256 MiB by default). A crop that does not fit returns the whole stored
  JPEG unchanged, made standalone as tile_location describes it, with
  tile_region locating the tile, as JPEG 2000 and JPEG XR crops do;
  jpegtran -crop can cut it. So does a crop whose output would exceed the
  encoded-unit limit. Apart from the usual admission limits, only a stored
  JPEG over the encoded-unit limit, or a tile spanning several JPEG strips
  whose crop does not fit, returns WsiError::ResourceLimit. TIFF LZW,
  Deflate, Zstd, uncompressed and JPEG XR tiles, DICOM native and RLE frames, MIRAX PNG and
  BMP records, CZI subblocks, Hamamatsu VMU and Zeiss ZVI planes now pass
  through. Tiles of lossless codecs that cannot be returned as stored come
  back as exact uncompressed samples.
• SlideLimits::lossless_crop_bytes and with_lossless_crop_bytes set the
  working set of a lossless JPEG crop in a raw tile read, 256 MiB by default,
  so 4096x4096 4:4:4 sources and large NDPI levels crop. Raw reads that may
  crop reserve it as per-operation transient work, so it must stay within
  operation_transient_bytes (384 MiB); decoded reads and other raw reads
  do not reserve it. encoded_unit_bytes still caps every stored unit.
  Custom SlideReaders admitted at the encoded-unit limit can ask for more
  for a raw read with SlideReader::raw_compressed_tile_reservation_hint.
• Python: Slide.tile_location, Slide.level_tile_locations and
  CompressedTile.tile_region, with a kerchunk-style reference example in the
  Python README. The tile_locations example checks reported ranges against
  read_raw_compressed_tile.
• Compression::Png, Compression::Bmp and
  EncodedTilePhotometricInterpretation::Monochrome1.
• Python wheels: publishing a GitHub release builds abi3 wheels for Python
  3.10 and later (Linux x86_64 and aarch64 on glibc 2.28 or newer, macOS
  arm64 and x86_64, Windows x64) and an sdist. Each wheel is tested, then all
  of them are attached to the release and published to PyPI as wsi-rs
  through trusted publishing, so pip install wsi-rs works. Pull requests
  that touch the bindings build and test the same wheels.

Changed

• Raw DICOM MONOCHROME1 tiles and raw grayscale TIFF JPEG tiles tagged
  MinIsWhite report EncodedTilePhotometricInterpretation::Monochrome1
  instead of Monochrome2.
• Raw TIFF JPEG and JPEG 2000 edge tiles report the size of the encoded
  image, which usually keeps the whole stored tile, with tile_region
  marking the clipped tile in it. They used to report the clipped size, which
  did not match the image the bytes decode to. A JPEG or codestream smaller
  than its tile returns an error.
• Raw Hamamatsu VMS tiles carry a JPEG header with the restart interval
  cleared, the same header tile_location reports. Only that header field
  changes; decoded pixels are unchanged.
• J2K dependencies follow the J2K main branch instead of the 0.8.1
  maintenance revision. Main carries the CUDA packet-header fix along with
  later decoder fixes and speedups.
• JXR follows its main branch, which builds on J2K main, so wsi-rs compiles
  one J2K instead of also J2K 0.12 for JXR. It requires JXR 0.4, the release
  line built on J2K 0.13.
• Builds take the newest J2K and JXR main commits: cargo latest updates
  them, and every CI job but packaging runs it before building; packaging
  checks the committed Cargo.lock. cargo-vet treats J2K and JXR
  as first-party code, reviewed in their own repositories, instead of
  requiring an audit for each revision.
• The J2K dependencies require 0.13.1, so a published wsi-rs resolves at
  least J2K 0.13.1, with its CPU and Metal batch region fixes, instead of
  accepting 0.13.0.
• Raw .j2k and .j2c levels with a side over 4096 pixels are read as
  1024 x 1024 tiles, each a region decode, instead of one tile covering the
  level, so a read decodes only the tiles it covers. A tile batch decodes its
  tiles serially side by side, where J2K decodes Tier-1 in bands as the inverse
  DWT reads them. Smaller levels still decode whole. Metal decodes tile batches
  at reductions up to 3 as one batch of regions sharing the codestream's bytes;
  deeper levels decode on the CPU. CUDA decoding is offered only when the full
  resolution is one tile. A raw read of a full-resolution tile returns the
  whole codestream with tile_region locating the tile; reduced resolutions
  have no raw read.

Fixed

• NDPI DCT retiling returns an error for an AC coefficient outside the
  8-bit baseline range, which it encoded wrongly, and for corrupt block grids,
  where it copied blocks wrapped from the next row.
• Merging TIFF JPEGTables into a tile shorter than its SOI marker returns
  an error instead of panicking.
• Raw .j2k and .j2c files whose decoded image exceeds 128 MiB, about 44.7
  megapixels of RGB, open. The decoded-image limit now bounds each decoded
  tile; it rejected the whole image at open. Reduced levels of such files
  decode, where they failed against the full-resolution size.
• A tile read from an uncompressed strip-based RGB TIFF reads only the rows it
  covers. It read the whole image, and read it again for every tile when the
  image was larger than the format cache.
• Some complete LZW-compressed TIFF tiles and strips failed to decode as
  truncated: J2K's LZW decoder stopped when the input ran out, before reading
  the end code in its last bytes. J2K main reads to the end code.