v0.2.0

• Search nested to process WSIs located in nested dirs (--search_nested)

• New caching mechanism to process very large batches of WSIs. When processing 100k+ WSIs, they are often stored on slow HDDs. To address this, use local caching on a fast SSD (--wsi_cache ./cache --cache_batch_size 32). Data will be copied automatically in batches, and processed in parallel. Automatic cleanup.

• New release() function in the Processor and WSI to ensure GPU memory is released.

• Version automatically inferred from the the toml file.

v0.1.1

Add readthedoc documentation

v0.1.0

• Added native support for CuCIM and PIL.

• All segmentation models now use Hugging Face and support local checkpoints (no more torch.hub).

• All patch models migrated to Hugging Face with local support (except Hibou and MUSK).

• Improved error handling and enhanced docstrings.

v0.0.5

New AnyToTiffConverter. Handy to convert non openslide readable files into pyramidal tiff.

v0.0.4: Merge pull request #2 from mahmoodlab/more_models

Support for 7 additional patch encoders:

• hibou_l
• kaiko-vits8
• kaiko-vits16
• kaiko-vitb8
• kaiko-vitb16
• kaiko-vitl14
• lunit-vits8

Support for 1 additional slide encoder:

• madeleine (based on conch_v1 patch encoder with 256x256 patches at 10x)

v0.0.3: Merge pull request #7 from mahmoodlab/more_segmenters

• Support for one additional tissue vs segmentation model based on GrandQC (Nat. Comm, 2024, https://www.nature.com/articles/s41467-024-54769-y). Much faster. Very good for H&E. Very bad for IHC and special stains. Can be used with --segmenter grandqc

• Expose tissue confidence threshold. Default to 0.5 thresh. Reducing it to 0.4 in challenging cases seem to help. Tested in PDL-1 on 100 WSIs.

v0.0.2

• Better tutorials
• Cleaner API
• Heatmap viz

v0.0.1

Trident is up and running. Your new library for large-scale whole-slide image processing. Supports:

• Batch processing with error handling
• Tissue vs Background segmentation
• Tissue patching
• Patch encoding using one of 13 foundation models, including UNI, UNIv2, CONCH, Virchow, H-Optimus, GigaPath
• Slide encoding using Titan, PRISM, CHIEF, GigaPath.

Stay Tuned for Updates! We're cooking!