✨ Integrate SAM as an Interactive Segmentation Tool #918
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commit d315a5f415542890f351ddb07c771d62c278c2f2 Merge: dab2693 1a27178 Author: Musraf Basheer <Musraf.Basheer@warwick.ac.uk> Date: Fri Jan 24 15:07:28 2025 +0000 Merge branch 'sam-architecture' into develop commit dab2693 Merge: ca37400 8ff4f5e Author: mbasheer04 <78800844+mbasheer04@users.noreply.github.com> Date: Fri Jan 24 15:04:28 2025 +0000 Merge branch 'TissueImageAnalytics:develop' into develop commit 1a27178 Merge: 3b51acb 8ff4f5e Author: mbasheer04 <78800844+mbasheer04@users.noreply.github.com> Date: Fri Jan 24 14:57:22 2025 +0000 Merge branch 'TissueImageAnalytics:develop' into sam-architecture commit 3b51acb Author: Musraf Basheer <Musraf.Basheer@warwick.ac.uk> Date: Fri Jan 24 14:53:06 2025 +0000 Improved Engine commit 8ff4f5e Author: Mark Eastwood <20169086+measty@users.noreply.github.com> Date: Thu Jan 23 10:03:43 2025 +0000 📌 Pin `zarr<3.0.0` (TissueImageAnalytics#905) - `zarr>3.0.0` is not compatible yet commit 46d30f2 Merge: 1e136c5 ca37400 Author: Musraf Basheer <Musraf.Basheer@warwick.ac.uk> Date: Fri Jan 17 14:22:18 2025 +0000 Merge branch 'develop' into sam-architecture commit ca37400 Merge: 32cae0b f385ced Author: mbasheer04 <78800844+mbasheer04@users.noreply.github.com> Date: Fri Jan 17 14:18:47 2025 +0000 Merge pull request #1 from TissueImageAnalytics/develop Merge develop commit 1e136c5 Merge: 47a2190 bb9399d Author: Musraf Basheer <Musraf.Basheer@warwick.ac.uk> Date: Fri Jan 17 14:12:52 2025 +0000 Merge branch 'sam-architecture' of https://github.com/mbasheer04/tiatoolbox into sam-architecture commit 47a2190 Author: Musraf Basheer <Musraf.Basheer@warwick.ac.uk> Date: Fri Jan 17 14:08:11 2025 +0000 Improved engine & added unit tests commit f385ced Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri Jan 10 12:04:52 2025 +0000 :technologist: pre-commit autoupdate (TissueImageAnalytics#902) * 🧑💻 pre-commit autoupdate updates: - [github.com/executablebooks/mdformat: 0.7.19 → 0.7.21](hukkin/mdformat@0.7.19...0.7.21) - [github.com/astral-sh/ruff-pre-commit: v0.8.2 → v0.8.6](astral-sh/ruff-pre-commit@v0.8.2...v0.8.6) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 0ddd2b1 Author: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Date: Thu Dec 12 14:45:39 2024 +0000 🔖 Release 1.6.0 (TissueImageAnalytics#898) ## TIAToolbox v1.6.0 (2024-12-12) ### Major Updates and Feature Improvements - **Foundation Models Support via `timm` API** (TissueImageAnalytics#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`** (TissueImageAnalytics#716) - Improved performance on newer GPUs using `torch.compile`. - **Multichannel Input Support in `WSIReader`** (TissueImageAnalytics#742) - **AnnotationStore Filtering for Patch Extraction** (TissueImageAnalytics#822) - **Python 3.12 Support** - **Deprecation of Python 3.8 Support** - **CLI Response Time Improvements** (TissueImageAnalytics#795) ### API Changes - **Device Specification Update** (TissueImageAnalytics#882) - Replaced `has_gpu` with `device` for specifying GPU or CPU usage, aligning with PyTorch's `Model.to()` functionality. - **Windows Compatibility Enhancement** (TissueImageAnalytics#769) - Replaced `POWER` with explicit multiplication. ### Bug Fixes and Other Changes - **TIFFWSIReader Bound Reading Adjustment** (TissueImageAnalytics#777) - Fixed `read_bound` to use adjusted bounds. - Reduced code complexity in `WSIReader` (TissueImageAnalytics#814). - **Annotation Rendering Fixes** (TissueImageAnalytics#813) - Corrected rendering of annotations with holes. - **Non-Tiled TIFF Support in `WSIReader`** (TissueImageAnalytics#807, contributed by @GeorgeBatch) - **HoVer-Net Documentation Update** (TissueImageAnalytics#751) - Corrected class output information. - **Citation File Fix for `cffconvert`** (TissueImageAnalytics#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 (TissueImageAnalytics#796). - **JSON Extraction Fixes** (TissueImageAnalytics#772) - Restructured SQL expression construction for JSON properties with dots in keys. - **VahadaneExtractor Warning** (TissueImageAnalytics#871) - Added warning due to changes in `scikit-learn>0.23.0` dictionary learning (TissueImageAnalytics#382). - **PatchExtractor Error Message Refinement** (TissueImageAnalytics#883) - **Immutable Output Fix in `WSIReader`** (TissueImageAnalytics#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** (TissueImageAnalytics#811) **Full Changelog:** TissueImageAnalytics/tiatoolbox@v1.5.1...v1.6.0 commit a38d95f Author: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Date: Thu Dec 5 17:14:20 2024 +0000 [skip ci] 🐛 Fix `benchmarks/annotation_store.ipynb` (TissueImageAnalytics#894) - Fix `benchmarks/annotation_store.ipynb` errors commit 6b214fe Author: adamshephard <39619155+adamshephard@users.noreply.github.com> Date: Tue Dec 3 14:09:33 2024 +0000 📝 Add Example Notebook for Foundation Models (TissueImageAnalytics#887) - Add Example Notebook to explain how to use Foundation Models from `timm` module in TIAToolbox. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> commit 442bd3f Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue Dec 3 09:40:40 2024 +0000 :technologist: pre-commit autoupdate (TissueImageAnalytics#891) <!--pre-commit.ci start--> updates: - [github.com/executablebooks/mdformat: 0.7.18 → 0.7.19](hukkin/mdformat@0.7.18...0.7.19) --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> commit 741463c Author: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Date: Mon Dec 2 22:45:05 2024 +0000 :pushpin: Update `ruff` Version to `v0.8.1` (TissueImageAnalytics#890) - Update `ruff` Version to `v0.8.1` --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 9a62c10 Author: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Date: Mon Dec 2 17:11:39 2024 +0000 [skip ci] :memo: Update Jupyter Notebooks for Release `v1.6.0` (TissueImageAnalytics#885) - Update Jupyter Notebooks for the New Release - Fix issues with API changes e.g., device instead of ON_GPU flag. commit 4a1940d Author: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Date: Fri Nov 29 16:13:37 2024 +0000 :technologist: `torch.compile` is not compatible with Windows. (TissueImageAnalytics#888) - `torch.compile` is not currently compatible with Windows. See pytorch/pytorch#122094 commit 5f1cecb Author: Jiaqi-Lv <60471431+Jiaqi-Lv@users.noreply.github.com> Date: Fri Nov 29 14:37:39 2024 +0000 🧑💻 Refine `PatchExtractor` Error Message (TissueImageAnalytics#883) - Fix Misleading error message TissueImageAnalytics#881 commit 5beb119 Author: Musraf Basheer <Musraf.Basheer@warwick.ac.uk> Date: Tue Nov 26 18:47:14 2024 +0000 Initialised SAM Engine commit bb9399d Author: mbasheer04 <78800844+mbasheer04@users.noreply.github.com> Date: Fri Nov 22 19:26:45 2024 +0000 Created using Colab commit ca13e7f Author: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Date: Thu Nov 21 22:28:44 2024 +0000 ♻️ Update Changes from New Engine Design (TissueImageAnalytics#882) - Add changes from New engine design TissueImageAnalytics#578. This will not only simplify the PR but also keep the main repo up to date. - Refactor `model_to` to `model_abc` - Instead of `on_gpu` use `device` as an input in line with `PyTorch`. - `infer_batch` uses `device` as an input instead of `on_gpu` commit 91ca877 Merge: 1e27436 32cae0b Author: mbasheer04 <bmusraf1@gmail.com> Date: Thu Nov 21 21:03:41 2024 +0000 Merge branch 'develop' of https://github.com/TissueImageAnalytics/tiatoolbox into sam-architecture commit 1e27436 Author: mbasheer04 <bmusraf1@gmail.com> Date: Thu Nov 21 21:00:34 2024 +0000 Implementing architecture for full-image segmentation commit 32cae0b Author: Abdol <a@fkrtech.com> Date: Fri Nov 15 20:29:34 2024 +0000 ⚡️Add `torch.compile` Functionality (TissueImageAnalytics#716) - Integrates PyTorch 2.0's [torch.compile](https://pytorch.org/docs/stable/generated/torch.compile.html) functionality to demonstrate performance improvements in torch code. This PR focuses on adding `torch.compile` to `PatchPredictor`. **Notes:** - According to the [documentation](https://pytorch.org/tutorials/intermediate/torch_compile_tutorial.html), noticeable performance can be achieved when using modern NVIDIA GPUs (H100, A100, or V100) **TODO:** - [x] Resolve compilation errors related to using `torch.compile` in running models - [x] Initial config - [x] Add to patch predictor - [x] Add to registration - [x] Add to segmentation - [x] Test on custom models - [x] Test on `torch.compile` compatible GPUs --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: Jiaqi-Lv <60471431+Jiaqi-Lv@users.noreply.github.com> commit e1a57c6 Author: mbasheer04 <bmusraf1@gmail.com> Date: Fri Nov 15 17:29:44 2024 +0000 Created Jupyter Notebook for SAM architecture commit 9113996 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri Nov 15 17:18:16 2024 +0000 :technologist: pre-commit autoupdate (TissueImageAnalytics#880) * 🧑💻 pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.0 → v0.7.2](astral-sh/ruff-pre-commit@v0.7.0...v0.7.2) * 📌 Update `ruff` version. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> commit c980eec Author: George Batchkala <46561186+GeorgeBatch@users.noreply.github.com> Date: Fri Nov 15 16:31:42 2024 +0000 🆕 Integrate Foundation Models Available VIA `timm`: `UNI`, `Prov-GigaPath`, `H-optimus-0` (TissueImageAnalytics#856) - Integrates pre-trained foundation models from other labs into tiatoolbox.models.architecture.vanilla.py. Currently, the `_get_architecture()` function allows the use of models from `torchvision.models`. A new function `_get_timm_architecture()` has been incorporated to support foundation models which are available from `timm` with weights on HuggingFace Hub. - All the models from `timm` that used require users to sign the licence agreement with the authors. - The users can add new models by modifying `_get_timm_architecture()` --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> commit 7fb9926 Author: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com> Date: Fri Nov 8 17:25:02 2024 +0000 🐛 Add Warning for `VahadaneExtractor` Algorithm Instability (TissueImageAnalytics#871) - Adds a warning to the `VahadaneExtractor` to inform users about the algorithm's instability due to changes in the dictionary learning algorithm in `scikit-learn versions > 0.23.0 (see issue TissueImageAnalytics#382)`. - The docstrings are updated accordingly to reflect this warning. - No other functionality is altered. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit f4f2fa6 Author: mbasheer04 <bmusraf1@gmail.com> Date: Sun Nov 3 23:41:50 2024 +0000 Initial setup of SAM architecture commit 12d435e Author: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Date: Thu Oct 24 16:40:56 2024 +0100 :pushpin: Pin `numpy<2.0.0` (TissueImageAnalytics#876) - `numpy>=2.0` breaks the tests. commit 76f02f8 Author: Mark Eastwood <20169086+measty@users.noreply.github.com> Date: Fri Oct 18 14:53:49 2024 +0100 🆕 Use Annotations as a Filter for Patch Extraction (TissueImageAnalytics#822) - Adds the ability to get patches filtered by class or label using AnnotationStore. - Allows the user to provide a path to an annotation store as the mask. - By default the mask will then be built out of all the annotations, but the user can also provide any filter that works in the annotation store, and have only those annotations make the mask. For example, if the user have some pathologist annotations with some regions, and they would only want to extract patches which have some overlap with regions labelled 'tumor' or any other class, they would just need to provide the appropriate string ("props['label'] == 'tumor'" for example). --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> commit 0b857c7 Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri Oct 18 12:00:04 2024 +0100 :technologist: `pre-commit` autoupdate (TissueImageAnalytics#868) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.6.0...v5.0.0) - [github.com/astral-sh/ruff-pre-commit: v0.6.5 → v0.6.9](astral-sh/ruff-pre-commit@v0.6.5...v0.6.9) * 🐛 Fix pre-commit yaml * 🧑💻 Change to monthly schedule. * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/executablebooks/mdformat: 0.7.17 → 0.7.18](hukkin/mdformat@0.7.17...0.7.18) - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.6.0...v5.0.0) - [github.com/astral-sh/ruff-pre-commit: v0.6.5 → v0.6.9](astral-sh/ruff-pre-commit@v0.6.5...v0.6.9) * 🔀 Merge online and local copies * 📌 Pin dependencies * 📌 Pin `ruff` version --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> commit 52792bc Author: Alon Alexander <alon008@gmail.com> Date: Wed Oct 2 12:51:52 2024 +0300 🐛 Fix `CITATION.cff` to Make it Compatible with `cffconvert` - To cite this repository using `cffconvert`, the conversion fails as the citation file was invalid. - This PR fixes the citation file to a valid ORCID. commit 3714ef7 Author: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Date: Wed Oct 2 10:22:26 2024 +0100 :pushpin: Pin `bokeh` version to less than 3.6.0 (TissueImageAnalytics#870) - Pin `bokeh` version to less than `3.6.0` - `bokeh` 3.6.0 has breaking changes
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| def predict_wsi(self, file_name, device="cpu", save_path=None): | ||
| return self.predict(file_name, device=device, save_path=save_path) | ||
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| def to_annotation(self, mask_path, score_path, save_filename: Path | str = None): |
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Move it to tiatoolbox.utils.misc.py
Removing large files Removing unneccessary files Fixing pre-commit [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Fixing PR issues :technologist: pre-commit autoupdate (TissueImageAnalytics#910) * 🧑💻 pre-commit autoupdate updates: - [github.com/executablebooks/mdformat: 0.7.21 → 0.7.22](hukkin/mdformat@0.7.21...0.7.22) - [github.com/astral-sh/ruff-pre-commit: v0.8.6 → v0.9.4](astral-sh/ruff-pre-commit@v0.8.6...v0.9.4) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 📌 Update `ruff` dependency * 🔥 TIAToolbox does not support Python > 3.12 yet - There is no need for this check as this will be tested while upgrading to Python 3.13 * ♻️ Refactor `typing` to `type_hints`. * 🐛 Fix `mypy` workflow --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> 📝 Update Documentation Structure (TissueImageAnalytics#909) - Use `Python 3.12` for docs build - Update `copyright` year to `2025` - Landing page now shows text from README - Update documentation structure - Update `readthedocs` Build - Remove `usage.rst` - Rename Jupyter Notebooks to Usage Examples - Show README for Usage Examples instead of TOC - Reduce TOC depth for basic functionalities and pipelines - Improve `README` quality. 🐛 Fix in `test_arch_mapde` and `test_arch_sccnn` (TissueImageAnalytics#911) - If cuda is available model should be moved to cuda otherwise tests will fail as test data is moved to cuda. [skip ci] 📝 Improve Documentation (TissueImageAnalytics#913) - Update CONTRIBUTING.rst - Bug fix in conf.py to fix notebook links - Update `examples/README.md` - Update `docs/installation.rst` - Update `docs/visualization.rst` --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com> :bug: Fix `MapDe` `dist_filter` Shape (TissueImageAnalytics#914) - Fix `dist_filter` in `MapDe` model for multi-class output. Explanation: Previously, if we set `num_class` to more than 1, the model would still output 1 channel. This was because the `dist_filter` always had size of 1 in its first dimension, however the first dimension determines the number of output channels in the tensor produced by `torch.functional.F.conv2d`. This PR changes this by repeating the filters the match the number of output classes. :technologist: pre-commit autoupdate (TissueImageAnalytics#916) * 🧑💻 pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.9.4 → v0.9.9](astral-sh/ruff-pre-commit@v0.9.4...v0.9.9) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 🔨 Update `ruff` version * 🔨 Update noqa for Unused static method argument --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Add FsspecJsonWSIReader class. (TissueImageAnalytics#897) The `FsspecJsonWSIReader` reads fsspec json file which represents SVS or TIFF whole slide image. The images are accessible by HTTP range requests, eg: `https://api.gdc.cancer.gov/data/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27` The whole image can be downloaded like: `curl -C - -o TCGA-22-1017-01Z-00-DX1.9562FE79-A261-42D3-B394-F3E0E2FF7DDA.svs https://api.gdc.cancer.gov/data/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27` The `FsspecJsonWSIReader` class has a `_zarr_store` field which is created by reading json file using `fsspec`: ``` mapper = fsspec.get_mapper( "reference://", fo=str(input_img), target_protocol="file" ) self._zarr_array = zarr.open(mapper, mode="r") self._zarr_store = self._zarr_array.store self._zarr_lru_cache = zarr.LRUStoreCache(self._zarr_store, max_size=cache_size) self._zarr_group = zarr.open(self._zarr_lru_cache) ``` This is equivalent to `TIFFWSIReader` code: ``` self._zarr_store = tifffile.imread( self.input_path, series=self.series_n, aszarr=True, ) self._zarr_lru_cache = zarr.LRUStoreCache(self._zarr_store, max_size=cache_size) self._zarr_group = zarr.open(self._zarr_lru_cache) ``` Both FsspecJsonWSIReader and TIFFWSIReader forward calls to `read_bounds` and `read_rect` methods of the`TIFFWSIReaderDelegate` delegate instance. The method `_info` of the`TIFFWSIReaderDelegate` reads SVS metadata which is stored in the root group metadata like: ``` { ".zattrs": { "multiscales": [ { "metadata": { "objective_power": 40, "vendor": "Aperio", "mpp": [0.2525, 0.2525] } } ] } } ``` To test, execute from the root dir: ``` pip install -r requirements/requirements_dev.txt mkdir -p samples/slides mkdir -p samples/fsspec cd samples/slides curl -C - -o TCGA-22-1017-01Z-00-DX1.9562FE79-A261-42D3-B394-F3E0E2FF7DDA.svs https://api.gdc.cancer.gov/data/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27 cd ../../ cp tiatoolbox/utils/tiff_to_fsspec.py . python tiff_to_fsspec.py "samples/slides/TCGA-22-1017-01Z-00-DX1.9562FE79-A261-42D3-B394-F3E0E2FF7DDA.svs" "samples/fsspec/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27_fsspec.json" "https://api.gdc.cancer.gov/data/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27" ``` Create `tileserver.py` inside of the project root: ``` from flask_cors import CORS from tiatoolbox.visualization import TileServer from tiatoolbox.wsicore.wsireader import FsspecJsonWSIReader wsi = FsspecJsonWSIReader.open( "./samples/fsspec/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27_fsspec.json" ) tile_server = TileServer( title="Tiatoolbox TileServer", layers={"layer": wsi}, ) CORS(tile_server, send_wildcard=True) tile_server.run(host="127.0.0.1", port=5000) ``` Open `http://127.0.0.1:5000/` and verify that it works. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> ✨ Support for Additional Foundation Models (TissueImageAnalytics#906) - Add support for additional foundation models as feature extractors using the TimmBackbone. - Added models include: UNI2, Virchow, Virchow2, kaiko and H-optimus-1. - Add more information to docstrings. - Allow foundation models with additional parameters. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Fixing PR issues
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This PR is a first draft for integrating the Segment Anything Model (SAM) into the TIAToolbox as an interactive prompt-based segmentation tool. Most of the functionality has been implemented, however measures need to be taken in order to make the project more robust. This PR is part of a final-year undergraduate project.
The changes include:
Things to be done: