Preparing for PR

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 (#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 (#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` (#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 (#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  (#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 (#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. (#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 (#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

Author: mbasheer04

.github/workflows/mypy-type-check.yml

@@ -40,7 +40,7 @@ jobs:
         mypy --install-types --non-interactive --follow-imports=skip \
           tiatoolbox/__init__.py \
           tiatoolbox/__main__.py \
-          tiatoolbox/typing.py \
+          tiatoolbox/type_hints.py \
           tiatoolbox/tiatoolbox.py \
           tiatoolbox/utils \
           tiatoolbox/tools \

.github/workflows/python-package.yml

@@ -30,7 +30,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.8.2 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.9.9 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
         - mdformat-black
         - mdformat-myst
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.21
+    rev: 0.7.22
     hooks:
     - id: mdformat
       # Optionally add plugins
@@ -60,7 +60,7 @@ repos:
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.8.6
+    rev: v0.9.9
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

.readthedocs.yml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.10"
+    python: "3.12"
   apt_packages:
     - openslide-tools
     - libopenjp2-7-dev

CONTRIBUTING.rst

@@ -1,11 +1,10 @@
 .. highlight:: shell
 
-============
+=============
 Contributing
-============
+=============
 
-Contributions are welcome, and they are greatly appreciated! Every little bit
-helps, and credit will always be given.
+Contributions are welcome and greatly appreciated! Every little bit helps, and credit will always be given.
 
 You can contribute in many ways:
 
@@ -26,21 +25,17 @@ If you are reporting a bug, please include:
 Fix Bugs
 ~~~~~~~~
 
-Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
-wanted" is open to whoever wants to implement it.
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help wanted" is open to whoever wants to implement it.
 
 Implement Features
 ~~~~~~~~~~~~~~~~~~
 
-Look through the GitHub issues for features. Anything tagged with "enhancement"
-and "help wanted" is open to whoever wants to implement it.
+Look through the GitHub issues for features. Anything tagged with "enhancement" and "help wanted" is open to whoever wants to implement it.
 
 Write Documentation
 ~~~~~~~~~~~~~~~~~~~
 
-TIA Toolbox could always use more documentation, whether as part of the
-official TIA Toolbox docs, in docstrings, or even on the web in blog posts,
-articles, and such.
+TIA Toolbox could always use more documentation, whether as part of the official TIA Toolbox docs, in docstrings, or even on the web in blog posts, articles, and such.
 
 Submit Feedback
 ~~~~~~~~~~~~~~~
@@ -50,9 +45,8 @@ The best way to send feedback is to file an issue at https://github.com/TissueIm
 If you are proposing a feature:
 
 * Explain in detail how it would work.
-* Keep the scope as narrow as possible, to make it easier to implement.
-* Remember that this is a volunteer-driven project, and that contributions
-  are welcome :)
+* Keep the scope as narrow as possible to make it easier to implement.
+* Remember that this is a volunteer-driven project, and contributions are welcome :)
 
 Get Started!
 ------------
@@ -64,7 +58,7 @@ Ready to contribute? Here's how to set up ``tiatoolbox`` for local development.
 
     $ git clone git@github.com:your_name_here/tiatoolbox.git
 
-3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+3. Install your local copy into a virtual environment. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
 
     $ mkvirtualenv tiatoolbox
     $ cd tiatoolbox/
@@ -76,13 +70,18 @@ Ready to contribute? Here's how to set up ``tiatoolbox`` for local development.
 
    Now you can make your changes locally.
 
-5. When you're done making changes, check that your changes pass flake8 and the
-   tests::
+5. When you're done making changes, check that your changes pass pre-commit and the tests::
 
-    $ flake8 tiatoolbox tests
+    $ pre-commit run --all-files
     $ python setup.py test or pytest
 
-   To get flake8, just pip install them into your virtualenv.
+   To get `pre-commit <https://pre-commit.com/#install>`_, just pip install it into your virtual environment using::
+
+    $ pip install pre-commit
+
+   To set up the git hook for pre-commit, run the following command after installing pre-commit::
+
+    $ pre-commit install
 
 6. Commit your changes and push your branch to GitHub::
 
@@ -98,20 +97,15 @@ Pull Request Guidelines
 Before you submit a pull request, check that it meets these guidelines:
 
 1. The pull request should include tests.
-2. If the pull request adds functionality, the docs should be updated. Put
-   your new functionality into a function with a docstring, and add the
-   feature to the list in README.rst.
-3. The pull request should work for Python 3.8, 3.9 and 3.10, and for PyPy. Check
-   https://travis-ci.com/tialab/tiatoolbox/pull_requests
-   and make sure that the tests pass for all supported Python versions.
+2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the pull request description.
+3. The pull request should work for Python 3.9, 3.10, 3.11, and 3.12, and for PyPy. Check https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml and make sure that the tests pass for all supported Python versions.
 
 Tips
 ----
 
 To run a subset of tests::
 
-$ pytest tests.test_tiatoolbox
-
+    $ pytest tests.test_tiatoolbox
 
 Deploying
 ---------
@@ -120,8 +114,8 @@ A reminder for the maintainers on how to deploy.
 Make sure all your changes are committed (including an entry in HISTORY.rst).
 Then run::
 
-$ poetry version patch # use: "poetry version --help" for other options
-$ git push
-$ git push --tags
+    $ poetry version patch  # use: "poetry version --help" for other options
+    $ git push
+    $ git push --tags
 
-Travis will then deploy to PyPI if tests pass.
+GitHub Actions will then deploy to PyPI if tests pass.

README.md

@@ -45,25 +45,21 @@
 
 ## Getting Started
 
-TIAToolbox is a computational pathology toolbox developed by TIA Centre that provides an end-to-end API for pathology image analysis using best practices. It is based on **[PyTorch](https://pytorch.org/)**, a popular deep learning framework that enables efficient and flexible implementation of state-of-the-art algorithms. TIAToolbox supports many features through a command-line interface and can integrate with standard PyTorch modules. It also offers tools for data loading, pre-processing, model inference, post-processing, and visualization. Whether you are a computational, biomedical, or clinical researcher, TIAToolbox can help you get started in digital pathology with minimal effort.
+TIAToolbox is a computational pathology toolbox developed by the TIA Centre. It provides an end-to-end API for pathology image analysis using best practices. Based on **[PyTorch](https://pytorch.org/)**, a popular deep learning framework, TIAToolbox enables efficient and flexible implementation of state-of-the-art algorithms. It supports many features through a command-line interface and can integrate with standard PyTorch modules. The toolbox offers tools for data loading, pre-processing, model inference, post-processing, and visualization. Whether you are a computational, biomedical, or clinical researcher, TIAToolbox can help you get started in digital pathology with minimal effort.
 
 ### All Users
 
-This package is for those interested in digital pathology: including graduate students, medical staff, members of the TIA Centre and of PathLAKE, and anyone, anywhere, who may find it useful. We will continue to improve this package, taking account of developments in pathology, microscopy, computing and related disciplines. Please send comments and criticisms to **[tia@dcs.warwick.ac.uk](mailto:tialab@dcs.warwick.ac.uk)**.
-
-**`tiatoolbox`** is a multipurpose name that we use for 1) a certain computer program, 2) a Python package of related programs, created by us at the TIA Centre to help people get started in Digital Pathology, 3) this repository, 4) a certain virtual environment.
+This package is designed for those interested in digital pathology, including graduate students, medical staff, members of the TIA Centre and PathLAKE, and anyone who may find it useful. We will continue to improve this package, taking into account developments in pathology, microscopy, computing, and related disciplines. Please send comments and feedback to **[tia@dcs.warwick.ac.uk](mailto:tialab@dcs.warwick.ac.uk)**.
 
 ### Developers
 
-Anyone wanting to contribute to this repository, please first look at our [Wiki](https://github.com/TissueImageAnalytics/tiatoolbox/wiki) and at our web page for [contributors](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/CONTRIBUTING.rst). See also the *Prepare for development* section of this document.
-
-### Links, if needed
+If you want to contribute to this repository, please first look at our [Wiki](https://github.com/TissueImageAnalytics/tiatoolbox/wiki) and our [contributor guidelines](https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/CONTRIBUTING.rst). Also, see the *Prepare for development* section of this document.
 
-The [bash](https://www.gnu.org/software/bash) shell is available on all commonly encountered platforms. Commands in this README are in bash. Windows users can use the command prompt to install conda and python packages.
+### Useful Links
 
-[conda](https://github.com/conda/conda) is a management system for software packages and [virtual environments](https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html). To get `conda`, download [Anaconda](https://www.anaconda.com/), which includes hundreds of the most useful Python packages, using 2GB disk space. Alternatively, [miniconda](https://docs.conda.io/en/latest/miniconda.html) uses 400MB, and packages can be added as needed.
+The [bash](https://www.gnu.org/software/bash) shell is available on all commonly encountered platforms. Commands in this README are in bash. Windows users can use the command prompt to install conda and Python packages.
 
-[GitHub](https://github.com/about) is powered by the version control system [git](https://git-scm.com/), which has many users and uses. In GitHub, it is used to track versions of code and other documents.
+[conda](https://github.com/conda/conda) is a management system for software packages and [virtual environments](https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html). To get `conda`, download [Anaconda](https://www.anaconda.com/), which includes hundreds of the most useful Python packages, using 2GB of disk space. Alternatively, [miniconda](https://docs.conda.io/en/latest/miniconda.html) uses 400MB, and packages can be added as needed.
 
 ### Examples Taster
 
@@ -130,7 +126,7 @@ or
 
 ### License
 
-The source code TIA Toolbox (tiatoolbox) as hosted on GitHub is released under the [BSD-3-Clause license](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/LICENSE). The full text of the licence is included in [LICENSE](https://raw.githubusercontent.com/TissueImageAnalytics/tiatoolbox/develop/LICENSE).
+The source code TIAToolbox (tiatoolbox) as hosted on GitHub is released under the [BSD-3-Clause license](https://github.com/TissueImageAnalytics/tiatoolbox/blob/develop/LICENSE). The full text of the licence is included in [LICENSE](https://raw.githubusercontent.com/TissueImageAnalytics/tiatoolbox/develop/LICENSE).
 
 Models weights are dependent on the datasets that they were trained on. Please refer to the [documentation](https://tia-toolbox.readthedocs.io/en/latest/pretrained.html) for more details.
 

docs/basic_functionalities.rst

@@ -2,7 +2,7 @@ Basic Functionalities
 *********************
 
 .. toctree::
-    :maxdepth: 2
+    :maxdepth: 1
     :glob:
 
     _notebooks/jnb/*

docs/conf.py

@@ -84,7 +84,7 @@
 
 # General information about the project.
 project = "TIA Toolbox"
-copyright = "2023, TIA Lab"
+copyright = "2025, TIA Lab"
 author = "TIA Lab"
 
 # The version info for the project you're documenting, acts as replacement
@@ -2005,8 +2005,8 @@ def all_but_ipynb(dir_path, contents):
 )
 
 # shutil.copy(
-#     os.path.join(PROJ_ROOT, "docs/notebooks.rst"),
-#     os.path.join(PROJ_ROOT, "docs/_notebooks/notebooks.rst"),
+#     os.path.join(PROJ_ROOT, "docs/usage_examples.rst"),
+#     os.path.join(PROJ_ROOT, "docs/_notebooks/usage_examples.rst"),
 # )
 
 # Read in the file
@@ -2016,8 +2016,8 @@ def all_but_ipynb(dir_path, contents):
 # Replace the target string
 file_data = file_data.replace(".rst", ".html")
 file_data = file_data.replace(".ipynb", ".html")
-file_data = file_data.replace("../docs/", "../")
-file_data = file_data.replace("](./", "](./jnb/")
+file_data = file_data.replace("](./", "](./_notebooks/jnb/")
+file_data = file_data.replace("../docs/", "./")
 
 # Write the file out again
 with open("_notebooks/README.md", "w") as file:

docs/index.rst

@@ -1,18 +1,19 @@
 Welcome to TIA Toolbox's documentation!
 =======================================
 
-.. image:: tia_logo.png
-    :alt: alternate text
-    :align: center
+.. include:: ../README.md
+   :parser: myst_parser.sphinx_
+
+Index
+-----
 
 .. toctree::
-    :maxdepth: 2
+    :maxdepth: 1
 
     Readme <readme.rst>
     Installation <installation.rst>
-    Usage <usage.rst>
     Pre-trained Models <pretrained.rst>
-    Jupyter Notebooks <notebooks.rst>
+    Usage Examples <usage_examples.rst>
     Algorithms <algorithms.rst>
     Visualization <visualization.rst>
     API Reference <_autosummary/tiatoolbox>