Release TIAToolbox 1.5.0 · TissueImageAnalytics/tiatoolbox

1.5.0 (2023-12-15)

Adds the bokeh visualization tool. #684
- The tool allows a user to launch a server on their machine to visualise whole slide images, overlay the results of deep learning algorithms or to select a patch from whole slide image and run TIAToolbox deep learning engines.
- This tool powers the TIA demos server. For details please see https://tiademos.dcs.warwick.ac.uk/.
Extends Annotation to Support Init from WKB #639
Adds IOConfig for NuClick in pretrained_model.yaml #709
Adds functions to save the TIAToolbox Engine outputs to Zarr and AnnotationStore files. #724
Adds Support for QuPath Annotation Imports #721

Adds model.to(device) and model.load_model_from_file() functionality to make it compatible with PyTorch API. #733
Replaces pretrained with weights to make the engines compatible with the new PyTorch API. #621
Adds support for high-level imports for various utility functions and classes such as WSIReader, PatchPredictor and imread #606, #607,
Adds tiatoolbox.typing for type hints. #619
Fixes incorrect file size saved by save_tiles, issue with certain WSIs raised by @TomastpPereira
TissueMasker transform now returns mask instead of a list. #748
- Fixes #732

Fixes pixman incompability error on Colab #601
Removes shapely.speedups. The module no longer has any affect in Shapely >=2.0. #622
Fixes errors in the slidegraph example notebook #608
Fixes bugs in WSI Registration #645, #670, #693
Fixes the situation where PatchExtractor.get_coords() can return patch coords which lie fully outside the bounds of a slide. #712
- Fixes #710
Fixes #738 raised by @xiachenrui

Replaces flake8 and isort with ruff #625, #666
Adds mypy checks to root and utils package. This will be rolled out in phases to other modules. #723
Adds a module to detect file types using magic number/signatures #616
Uses poetry for version updates instead of bump2version. #638
Removes setup.cfg and uses pyproject.toml for project configurations.
Reduces runtime for some unit tests e.g., #627, #630, #631, #629
Reuses models and datasets in tests on GitHub actions by utilising cache #641, #644
Set up parallel tests locally #671

Full Changelog: v1.4.0...v1.5.0