🔖 Release 2.0.0 by shaneahmed · Pull Request #1033 · TissueImageAnalytics/tiatoolbox

shaneahmed · 2026-03-11T21:58:28Z

TIAToolbox v2.0.0 (2026-03-11)

✨ Major Updates and Feature Improvements

⚙️ Engine Redesign (PR #578)

TIAToolbox 2.0.0 introduces a completely re-engineered inference engine designed for significant performance, scalability, and memory-efficiency improvements.

Key Enhancements

A modern processing stack built on Dask (parallel/distributed execution) and Zarr (chunked, out-of-core storage)
Standardised output formats across all engines:
- Python dict
- Zarr
- AnnotationStore (SQLite-backed)
- QuPath JSON
Cleaner runtime behavior with reduced warning noise and a unified progress bar
More predictable memory usage through chunked streaming
Broader test coverage across engine components

🗺️ Improved QuPath Support

Enhancements include:

Better handling of GeoJSON
Support for multipoint geometries (🆕 Improve Support for QuPath GeoJson and Multipoint Geometry #841)
Improved semantic output helpers:
- dict_to_store_semantic_segmentor (✨ Add dict_to_store_semantic_segmentor #926)
- OME-TIFF probability overlays (✨ Add Feature to Write Model Probabilities as ome.tiff for Overlay #929)

🔬 New Nucleus Detection Engine

A dedicated nucleus detection pipeline has been added, built on the redesigned engine for improved accuracy and efficient large-scale processing.

🧠 KongNet Model Family

TIAToolbox 2.0.0 introduces KongNet, a high-performance architecture that achieved top results across multiple international challenges:

🥇 1st place: MONKEY Challenge (overall detection)
🥇 1st place: MIDOG (mitosis detection)
⭐ Top-tier performance on PUMA

Multiple pretrained variants are available (CoNIC, PanNuke, MONKEY, PUMA, MIDOG), each with standardised IO configurations.

🧬 Expanded Foundation Model Support

Additional foundation models are now supported (#906), broadening the range of high-capacity architectures available for feature extraction and downstream tasks.

🖼️ SAM Segmentation in TIAViz

TIAViz now integrates Meta’s Segment Anything Model (SAM), enabling:

Interactive segmentation
Rapid region extraction
Exploratory annotation workflows

Simplified SAM usage (#968) streamlines its integration into analysis pipelines.

🖼️ WSI Registration Visualization in TIAViz

TIAViz now supports interactive WSI registration visualisation, allowing users to compare aligned slides in two modes:

Side‑by‑side view — view fixed and moving WSIs next to each other for direct comparison
Overlay mode — blend registered WSIs with adjustable transparency for visual inspection of alignment quality

This feature enables intuitive, high‑resolution exploration of slide registration results directly within TIAViz.

🧩 Enhanced WSIReader & Metadata Handling

Major improvements include:

More robust cross-vendor metadata extraction (⚡ Improve Metadata Handling for WSI Readers #1001)
Multichannel image support (PR 🆕Multichannel Image Reading #825) for immunofluorescence and non-RGB modalities
Simplified Windows installation using openslide-bin (no manual DLL steps)
macOS Tileserver fix (🔨 Fix TileServer issues on macOS #976)
Improved DICOM reading (🐛 Fix DICOM Reading (Issue #933) #934)

☁️ New Cloud-Native Reader: FsspecJSONWSIReader (PR #897)

A new reader supporting fsspec-compatible filesystems, enabling seamless access to WSIs stored on:

S3
GCS
Azure
HPC clusters
Any fsspec-supported backend

This enables cloud-native and distributed data workflows.
Contributed by @aacic

🤗 Pretrained Models Migrated to Hugging Face

All pretrained models and sample assets have been migrated (#945, #983), improving:

Download reliability
Versioning and reproducibility
Caching and CI integration
Licensing clarity per model family

🛡️ Security, Compatibility & Tooling

🔐 Security & Dependency Updates

Dependency upgrades
Internal security improvements
Explicit workflow permissions added (🛂 Fix Workflow Does Not Contain Permissions #1021, 🛂 Workflow Does Not Contain Permissions #1023)

🐍 Python Version Support

Dropped: Python 3.9
Added: Python 3.13
Supported: Python 3.10–3.13
Updated CUDA wheel source to cu126

🛠️ Developer Tooling & CI/CD

Expanded mypy type-checking coverage (🔧 mypy Type Check tiatoolbox/models #912, 🔧 mypy type check tools/ and utils/ #931, 🔧 mypy type check wsicore #935, 🏷️ mypy Update Typing in utils.py #951)
Updated pre-commit hooks and general formatting
CI uses CPU-only PyTorch for faster, more reliable builds (🧑‍💻 Use cpu-only PyTorch for GitHub Actions #974, 🧑‍💻 Update .readthedocs.yml to Install CPU Version only #979)
Updated pip install workflow (🧑‍💻 Update pip install Workflow #1013)
Added new Python 3.13 Docker images (⬆️ Update Docker Containers #1014, Improve Dockerfiles for Ubuntu #1019)

🧹 Bug Fixes & Stability Improvements

Fixed multi-GPU behaviour with torch.compile (🐛 Fix Multi-GPU Support with torch.compile #923)
Fixed DICOM reading issue (🐛 Fix DICOM Reading (Issue #933) #934)
Fixed annotation contour handling with holes (🐛 Fix Contours with Holes #956)
Fixed consecutive annotation load bug (🐛 Fix Consecutive Annotations Load Bug #927)
Fixed SCCNN model issues (🐛 Fix sccnn Model #970)
Fixed MapDe dist_filter shape issue (🐛 Fix MapDe dist_filter Shape #914)
Improved notebook reliability on Colab (✏️ Fix Notebook 11 Link #1026–🎨 Fix tqdm Progress Bar on Colab Runs #1030)
macOS TileServer issues resolved (🔨 Fix TileServer issues on macOS #976)

🧭 Migration Guide for Users

🔄 Updating from 1.x to 2.0.0

Update calls: replace `.predict()` with `.run()`

# Old
results = segmentor.predict(imgs=[...], ioconfig=config)

# New
results = segmentor.run(images=[...], ioconfig=config)

Use `patch_mode`: replace `mode="patch"` with `patch_mode=True` and `mode="tile"` or "wsi" with `patch_mode=False`

# Old
results = segmentor.predict(imgs=[...], mode="patch", ioconfig=config)

# New
results = segmentor.run(images=[...], patch_mode=True, ioconfig=config)

# Old
results = segmentor.predict(imgs=[...], mode="wsi", ioconfig=config)

# New
results = segmentor.run(images=[...], patch_mode=False, ioconfig=config)

Use the new I/O configs

from tiatoolbox.models.engine.io_config import IOSegmentorConfig

config = IOSegmentorConfig(
    patch_input_shape=(256, 256),
    stride_shape=(240, 240),
    input_resolutions=[{"resolution": 0.25, "units": "mpp"}],
    save_resolution={"units": "baseline", "resolution": 1.0},
)

Specify the output format

results = segmentor.run(
    images=[...],
    ioconfig=ioconfig,
    output_type="zarr",  # or "dict", "annotationstore", "qupath"
    save_dir="outputs/",
)

Update imports

tiatoolbox.typing → tiatoolbox.type_hints

Install requirements

Python 3.10+ required
On Windows: install OpenSlide via pip install openslide-bin

Full Changelog: v1.6.0...v2.0.0

@rogertrullo

### Major Updates and Feature Improvements - Adds an AnnotationTileGenerator and AnnotationRenderer which allows serving of tiles rendered directly from an annotation store. - Adds [DFBR](https://arxiv.org/abs/2202.09971) registration model and jupyter notebook example - Adds DICE metric - Adds [SCCNN](https://doi.org/10.1109/tmi.2016.2525803) architecture. \[[read the docs](https://tia-toolbox.readthedocs.io/en/develop/_autosummary/tiatoolbox.models.architecture.sccnn.SCCNN.html)\] - Adds [MapDe](https://arxiv.org/abs/1806.06970) architecture. \[[read the docs](https://tia-toolbox.readthedocs.io/en/develop/_autosummary/tiatoolbox.models.architecture.mapde.MapDe.html)\] - Adds support for reading MPP metadata from NGFF v0.4 - Adds enhancements to tiatoolbox.annotation.storage that are useful when using an AnnotationStore for visualization purposes. ### Changes to API - None ### Bug Fixes and Other Changes - Fixes colorbar_params #410 - Fixes Jupyter notebooks for better read the docs rendering - Fixes typos, metadata and links - Fixes nucleus_segmentor_engine for boundary artefacts - Fixes the colorbar cropping in tests - Adds citation in README.md and CITATION.cff to Nature Communications Medicine paper - Fixes a bug #452 raised by @rogertrullo where only the numerator of the TIFF resolution tags was being read. - Fixes HoVer-Net+ post-processing to be inline with original work. - Fixes a bug where an exception would be raised if the OME XML is missing objective power. ### Development related changes - Uses Furo theme for readthedocs - Replaces nbgallery and nbsphinx with myst-nb for jupyter notebook rendering - Uses myst for markdown parsing - Uses requirements.txt to define dependencies for requirements consistency - Adds notebook AST pre-commit hook - Adds check to validate python examples in the code - Adds check to resolve imports - Fixes an error in a docstring which triggered the failing test. - Adds pre-commit hooks to format markdown and notebook markdown - Adds pip install workflow to resolve dependencies when requirements file is updated - Improves TIAToolbox import using LazyLoader Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

# 1.3.1 (2022-12-20) ### Major Updates and Feature Improvements - Adds [NuClick](https://arxiv.org/abs/2005.14511) architecture #449 - Adds Annotation Store Reader #476 - Adds [DFBR](https://arxiv.org/abs/2202.09971) method for registering pair of images #510 ### Changes to API - Adds a sample SVS loading function `tiatoolbox.data.small_svs()` to the data module #517 ### Bug Fixes and Other Changes - Simplifies example notebook for image reading for better readability - Restricts Shapely version to \<2.0.0 for compatibility ### Development related changes - Adds GitHub workflow for automatic generation of docker image - Updates dependencies - Updates bump2version config - Enables flake8 E800 checks for commented codes. - Fixes several errors generated by DeepSource. - Prevent test dumping file to root - Removes duplicate functions to generate parameterized test scenarios Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: kesixu <98600542+kesixu@users.noreply.github.com> Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com> Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Roger Trullo <rogertrullo@hotmail.com>

- Adds [NuClick](https://arxiv.org/abs/2005.14511) architecture #449 - Adds Annotation Store Reader #476 - Adds [DFBR](https://arxiv.org/abs/2202.09971) method for registering pair of images #510 - Adds a sample SVS loading function `tiatoolbox.data.small_svs()` to the data module #517 - Simplifies example notebook for image reading for better readability - Restricts Shapely version to \<2.0.0 for compatibility - Adds GitHub workflow for automatic generation of docker image - Updates dependencies - Updates bump2version config - Enables flake8 E800 checks for commented codes. - Fixes several errors generated by DeepSource. - Prevent test dumping file to root - Removes duplicate functions to generate parameterized test scenarios Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: kesixu <98600542+kesixu@users.noreply.github.com> Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com> Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Roger Trullo <rogertrullo@hotmail.com>

- 🚑 Hotfix - Restricts wsidicom version to \<0.7.0 for compatibility - Fix bug related to reading DICOM files

## 1.3.3 (2023-03-02) ### Major Updates and Feature Improvements - Restricts dependency versions for long term stability of the current version ### Changes to API None ### Bug Fixes and Other Changes - Fix bug related to reading scikit-image ### Development related changes - Restricts dependency versions for compatibility

@navidstuv

## 1.4.0 (2023-04-24) ### Major Updates and Feature Improvements - Adds Python 3.11 support \[experimental\] #500 - Python 3.11 is not fully supported by `pytorch` pytorch/pytorch#86566 and `openslide` openslide/openslide-python#188 - Removes Python 3.7 support - This allows upgrading all the dependencies which were dependent on an older version of Python. - Adds Neighbourhood Querying Support To AnnotationStore #540 - This enables easy and efficient querying of annotations within a neighbourhood of other annotations. - Adds `MultiTaskSegmentor` engine #424 - Fixes an issue with stain augmentation to apply augmentation to only tissue regions. - #546 contributed by @navidstuv - Filters logger output to stdout instead of stderr. - Fixes #255 - Allows import of some modules at higher level for improved usability - `WSIReader` can now be imported as `from tiatoolbox.wsicore import WSIReader` - `WSIMeta` can now be imported as `from tiatoolbox.wsicore import WSIMeta` - `HoVerNet`, `HoVerNetPlus`, `IDaRS`, `MapDe`, `MicroNet`, `NuClick`, `SCCNN` can now be imported as \`from tiatoolbox.models import HoVerNet, HoVerNetPlus, IDaRS, MapDe, MicroNet, NuClick, SCCNN - Improves `PatchExtractor` performance. Updates `WSIPatchDataset` to be consistent. #571 - Updates documentation for `License` for clarity on source code and model weights license. ### Changes to API - Updates SCCNN architecture to make it consistent with other models. #544 ### Bug Fixes and Other Changes - Fixes Parsing Missing Omero Version NGFF Metadata #568 - Fixes #535 raised by @benkamphaus - Fixes reading of DICOM WSIs at the correct level #564 - Fixes #529 - Fixes `scipy`, `matplotlib`, `scikit-image` deprecated code - Fixes breaking changes in `DICOMWSIReader` to make it compatible with latest `wsidicom` version. #539, #580 - Updates `shapely` dependency to version >=2.0.0 and fixes any breaking changes. - Fixes bug with `DictionaryStore.bquery` and `geometry=None`, i.e. only a where predicate given. - Partly Fixes #532 raised by @blaginin - Fixes local tests for Windows/Linux - Fixes `flake8`, `deepsource` errors. - Uses `logger` instead of `warnings` and `print` statements to properly log runs. ### Development related changes - Upgrades dependencies which are dependent on Python 3.7 - Moves `requirements*.txt` files to `requirements` folder - Removes `tox` - Uses `pyproject.toml` for `bdist_wheel`, `pytest` and `isort` - Adds `joblib` and `numba` as dependencies.

### Bug Fixes and Other Changes - Fix dictionary changed size Error #626 (#605)

@TomastpPereira

## 1.5.0 (2023-12-15) ### Major Updates and Feature Improvements - 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 ### Changes to API - 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 ### Bug Fixes and Other Changes - 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 ### Development related changes - 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 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mostafajahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: DavidBAEpstein <David.Epstein@warwick.ac.uk> Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com> Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: adamshephard <adam.shephard@warwick.ac.uk> Co-authored-by: Abdol <a@fkrtech.com> Co-authored-by: Jiaqi-Lv <60471431+Jiaqi-Lv@users.noreply.github.com> Co-authored-by: Abishek <abishekraj6797@gmail.com> Co-authored-by: Dmitrii Blaginin <blaginin@mbp.lan>

## 1.5.1 (2023-12-16) ### Development related changes - Specifies compatible Python versions - Fixes `tiatoolbox-feedstock` build for conda-forge release #763 **Full Changelog:** v1.5.0...v1.5.1

@GeorgeBatch

## TIAToolbox v1.6.0 (2024-12-12) ### Major Updates and Feature Improvements - **Foundation Models Support via `timm` API** (#856, contributed by @GeorgeBatch) - Introduced `TimmBackbone` for running additional PyTorch Image Models. - Tested models include `UNI`, `Prov-GigaPath`, and `H-optimus-0`. - Added an example notebook demonstrating feature extraction with foundation models. - `timm` added as a dependency. - **Performance Enhancements with `torch.compile`** (#716) - Improved performance on newer GPUs using `torch.compile`. - **Multichannel Input Support in `WSIReader`** (#742) - **AnnotationStore Filtering for Patch Extraction** (#822) - **Python 3.12 Support** - **Deprecation of Python 3.8 Support** - **CLI Response Time Improvements** (#795) ### API Changes - **Device Specification Update** (#882) - Replaced `has_gpu` with `device` for specifying GPU or CPU usage, aligning with PyTorch's `Model.to()` functionality. - **Windows Compatibility Enhancement** (#769) - Replaced `POWER` with explicit multiplication. ### Bug Fixes and Other Changes - **TIFFWSIReader Bound Reading Adjustment** (#777) - Fixed `read_bound` to use adjusted bounds. - Reduced code complexity in `WSIReader` (#814). - **Annotation Rendering Fixes** (#813) - Corrected rendering of annotations with holes. - **Non-Tiled TIFF Support in `WSIReader`** (#807, contributed by @GeorgeBatch) - **HoVer-Net Documentation Update** (#751) - Corrected class output information. - **Citation File Fix for `cffconvert`** (#869, contributed by @Alon-Alexander) - **Bokeh Compatibility Updates** - Updated `bokeh_app` for compatibility with `bokeh>=3.5.0`. - Switched from `size` to `radius` for `bokeh>3.4.0` compatibility (#796). - **JSON Extraction Fixes** (#772) - Restructured SQL expression construction for JSON properties with dots in keys. - **VahadaneExtractor Warning** (#871) - Added warning due to changes in `scikit-learn>0.23.0` dictionary learning (#382). - **PatchExtractor Error Message Refinement** (#883) - **Immutable Output Fix in `WSIReader`** (#850) ### Development-Related Changes - **Mypy Checks Added** - Applied to `utils`, `tools`, `data`, `annotation`, and `cli/common`. - **ReadTheDocs PDF Build Deprecation** - **Formatter Update** - Replaced `black` with `ruff-format`. - **Dependency Removal** - Removed `jinja2`. - **Test Environment Update** - Updated to `Ubuntu 24.04`. - **Conda Environment Workflow Update** - Implemented `micromamba` setup. - **Codecov Reporting Fix** (#811) **Full Changelog:** v1.5.1...v1.6.0 --------- Co-authored-by: John Pocock <John-P@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Adam Shephard <39619155+adamshephard@users.noreply.github.com> Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com> Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com> Co-authored-by: Abdol A <u2271662@live.warwick.ac.uk> Co-authored-by: Jiaqi-Lv <60471431+Jiaqi-Lv@users.noreply.github.com> Co-authored-by: Dmitrii Blaginin <blaginin@mbp.lan> Co-authored-by: behnazelhaminia <30952176+behnazelhaminia@users.noreply.github.com> Co-authored-by: George Batchkala <46561186+GeorgeBatch@users.noreply.github.com> Co-authored-by: vqdang <24943262+vqdang@users.noreply.github.com> Co-authored-by: Jiaqi Lv <lvjiaqi9@gmail.com> Co-authored-by: Alon Alexander <alon008@gmail.com>

- Fix `pip install` Check for Windows

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This reverts commit c53a1d8.

This reverts commit 384f49e.

This reverts commit 770c0c6.

shaneahmed and others added 22 commits October 21, 2022 23:00

Merge remote-tracking branch 'origin/master'

ce788a3

🔖 REL: Release 1.3.2 (#541)

24390e5

- 🚑 Hotfix - Restricts wsidicom version to \<0.7.0 for compatibility - Fix bug related to reading DICOM files

🚑 Release 1.4.1 (#661)

51f504b

### Bug Fixes and Other Changes - Fix dictionary changed size Error #626 (#605)

🚑 Release 1.5.1 (#764)

490be26

## 1.5.1 (2023-12-16) ### Development related changes - Specifies compatible Python versions - Fixes `tiatoolbox-feedstock` build for conda-forge release #763 **Full Changelog:** v1.5.0...v1.5.1

🔀 Merge remote-tracking branch 'origin/master' into pre-release

85a8fe8

🔖 Bump up version to 2.0.0

3c83c98

🔖 Update Copyright year

9af2a8f

📝 Update Jupyter notebook links

384f49e

📝 Update Jupyter notebook installation instructions

c53a1d8

📌 Pin library versions in requirements.txt

770c0c6

📝 Update AUTHORS.md

5f4f365

📝 Update HISTORY.md

8613810

🔨 Fix pip install Check for Windows (#1032)

8097f62

- Fix `pip install` Check for Windows

📝 Fix HISTORY.md

a66f744

📝 Update AUTHORS.md

1c7c39c

shaneahmed self-assigned this Mar 11, 2026

shaneahmed added this to the Release v2.0.0 milestone Mar 11, 2026

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shaneahmed added 3 commits March 12, 2026 11:08

Revert ":memo: Update Jupyter notebook installation instructions"

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This reverts commit c53a1d8.

Revert ":memo: Update Jupyter notebook links"

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This reverts commit 384f49e.

Revert ":pushpin: Pin library versions in requirements.txt"

6dac340

This reverts commit 770c0c6.

📝 Update HISTORY.md

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shaneahmed merged commit ce9a2d0 into develop Mar 12, 2026
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🔖 Release 2.0.0#1033

🔖 Release 2.0.0#1033
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TIAToolbox v2.0.0 (2026-03-11)

✨ Major Updates and Feature Improvements

⚙️ Engine Redesign (PR #578)

Key Enhancements

🗺️ Improved QuPath Support

🔬 New Nucleus Detection Engine

🧠 KongNet Model Family

🧬 Expanded Foundation Model Support

🖼️ SAM Segmentation in TIAViz

🖼️ WSI Registration Visualization in TIAViz

🧩 Enhanced WSIReader & Metadata Handling

☁️ New Cloud-Native Reader: FsspecJSONWSIReader (PR #897)

🤗 Pretrained Models Migrated to Hugging Face

🛡️ Security, Compatibility & Tooling

🔐 Security & Dependency Updates

🐍 Python Version Support

🛠️ Developer Tooling & CI/CD

🧹 Bug Fixes & Stability Improvements

🧭 Migration Guide for Users

🔄 Updating from 1.x to 2.0.0

Update calls: replace .predict() with .run()

Use patch_mode: replace mode="patch" with patch_mode=True and mode="tile" or "wsi" with patch_mode=False

Use the new I/O configs

Specify the output format

Update imports

Install requirements

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shaneahmed commented Mar 11, 2026 •

edited

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Update calls: replace `.predict()` with `.run()`

Use `patch_mode`: replace `mode="patch"` with `patch_mode=True` and `mode="tile"` or "wsi" with `patch_mode=False`

codecov Bot commented Mar 11, 2026 •

edited

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