This is a minor, bug-fix release. See the Version 3.0 release notes for details about the latest major release.

Minor features

• Update cuCIM micron-per-pixel detection. When detecting MPP from TIFF metadata, recognize the singular form of units (centimeter, millimeter, micrometer) in addition to plural form [#420]
• Add show_progress keyword argument for the feature extractor tfrecord_inference() method, for optionally displaying a progress bar.
• Add new run_batched_inference() method to pytorch feature extractors, used for generating features from a large tensor dataset of images.
• When generating features (using a feature extractor) from a loaded pytorch tensor of images, add a new batch_size argument that runs batch inference, decreasing memory requirements:

  ctranspath = sf.build_feature_extractor('ctranspath')
  images = torch.load(...)
  features = ctranspath(images, batch_size=32)
  

Fixes

• Skip disk logs if Slideflow is in a read-only directory
• Fix rare TypeError: 'NoneType' object is not subscriptable error when attempting to get an image tile from a slide via indexing and the image tile is invalid (e.g. out of bounds; corrupted; etc)
• Minor fix to progress bar accuracy during bag generation
• Fix/remove lifelines requirement [#414]
• Add numpy 2.0 compatibility to PyTorch dataloaders
• Require spacy<3.8 to prevent numpy version incompatibility with FastAI
• Add pyarrow to requirements (required for parquet reading/writing)
• Fix dataset splitting for survival models
• Various unit test updates