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🔖 Release 2.1.0 (#1064)
## TIAToolbox v2.1.0 (2026-05-19) ### ✨ Major Updates and Feature Improvements - Python ≥3.11 required - Supports up to 3.14 (#1035) - Drops support for 3.10 (#1034) - Zarr v3 Support (#904) - New storage APIs (zarr.Array, LocalStore, FsspecStore) - Removal of object arrays → rectangular storage via pad_contours - Update `FsspecJsonWSIReader` to support Zarr v3 (#1049), thanks to @aacic ### ⚠️ API Changes - Python requirement updated → >=3.11, \<3.15 ### 🐞 Bug Fixes and Other Changes - Fixed - Contour serialization and padding issues (Zarr compatibility) (#904) - Invalid Geometry in JSON Outputs (#1057) - Fix typographical errors in `pre-trained` documentation (#1043, #1062) ### 🛠️ Development-Related Changes - Use `uv` to set up CI environments, reduces installation time - Update instructions for `uv` install - Use `max_image` for `remove_small_objects` in `scikit-image` usage (#1048) - Improve `mypy` workflow and typing errors (#1045) --------- Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com> Co-authored-by: measty <20169086+measty@users.noreply.github.com> Co-authored-by: Jiaqi-Lv <60471431+Jiaqi-Lv@users.noreply.github.com> Co-authored-by: Aleksandar Acic <32873451+aacic@users.noreply.github.com> 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> Co-authored-by: Aakash Madhav Rao <axr1154@student.bham.ac.uk> Co-authored-by: Yijie Zhu <120978607+YijieZhu15@users.noreply.github.com> Co-authored-by: gozdeg <gozdegunesli@gmail.com> Co-authored-by: Abdol A <u2271662@live.warwick.ac.uk> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>
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‎.github/workflows/conda-env-create.yml‎

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# This workflow will build a conda environment to check that it resolves in a reasonable time
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# This workflow will build a conda environment to check that it resolves
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name: Solve Conda Environment
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on:
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push:
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paths: [ "requirements/requirements*.yml", "conda-env-create.yml", "requirement*.txt"]
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paths:
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- "requirements/requirements*.txt"
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- "requirements/generate_conda_env.py"
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- ".github/workflows/conda-env-create.yml"
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pull_request:
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paths: [ "requirements/requirements*.yml", "conda-env-create.yml", "requirement*.txt"]
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schedule: # Run on the 1st of every month at midnight
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- cron: "0 0 1 * *"
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paths:
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- "requirements/requirements*.txt"
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- "requirements/generate_conda_env.py"
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- ".github/workflows/conda-env-create.yml"
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jobs:
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conda_solve:
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strategy:
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fail-fast: true
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fail-fast: false
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matrix:
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os: [ubuntu-latest, windows-latest]
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kind: ["dev", "prod"]
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include:
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- os: ubuntu-latest
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kind: prod
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requirements: requirements/requirements.conda.yml
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- os: ubuntu-latest
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kind: dev
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requirements: requirements/requirements.dev.conda.yml
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- os: windows-latest
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kind: prod
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requirements: requirements/requirements.win64.conda.yml
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- os: windows-latest
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kind: dev
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requirements: requirements/requirements.win64.dev.conda.yml
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os: [ubuntu-latest, windows-latest, macos-latest]
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python-version: ["3.11", "3.12", "3.13", "3.14"]
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runs-on: ${{ matrix.os }}
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timeout-minutes: 20
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timeout-minutes: 30
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steps:
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- uses: actions/checkout@v4
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- name: Copy requirements files
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shell: bash
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run: |
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cp ./requirements/requirements*.txt /tmp/
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mkdir /tmp/docs/
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cp ./docs/requirements*.txt /tmp/docs/
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# ✅ Generate environment
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- name: Generate conda environment
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env:
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PYTHON_VERSION: ${{ matrix.python-version }}
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run: python requirements/generate_conda_env.py
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# ✅ Install via micromamba
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- uses: mamba-org/setup-micromamba@v1
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with:
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environment-name: tiatoolbox
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environment-file: ${{ matrix.requirements }}
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- shell: bash -l {0}
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environment-file: requirements/requirements.conda.generated.yml
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# ✅ Validate environment
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- name: Test environment
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shell: bash -l {0}
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run: |
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micromamba info
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micromamba list
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python -c "import torch, numpy; print(torch.__version__, numpy.__version__)"
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python - <<EOF
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import sys
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print("Python:", sys.version)
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import numpy, pandas
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print("Core OK")
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try:
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import torch
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print("Torch OK")
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except Exception as e:
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print("Torch issue:", e)
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try:
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import cv2
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print("OpenCV OK")
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except Exception as e:
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print("OpenCV issue:", e)
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try:
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import openslide
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print("OpenSlide OK")
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except Exception as e:
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print("OpenSlide issue:", e)
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EOF

‎.github/workflows/docker-publish.yml‎

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REGISTRY: ghcr.io
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IMAGE_NAME: TissueImageAnalytics/tiatoolbox
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image: ghcr.io/tissueimageanalytics/tiatoolbox
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TOOLBOX_VER: 2.0.1
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TOOLBOX_VER: 2.1.0
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jobs:
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build-and-push-image:
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fail-fast: true
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matrix:
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include:
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- dockerfile: ./docker/3.10/Debian/Dockerfile
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mtag: py3.10-debian
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- dockerfile: ./docker/3.10/Ubuntu/Dockerfile
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mtag: py3.10-ubuntu
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- dockerfile: ./docker/3.11/Debian/Dockerfile
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mtag: py3.11-debian
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- dockerfile: ./docker/3.11/Ubuntu/Dockerfile

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

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strategy:
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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python-version: ["3.11", "3.12", "3.13", "3.14"]
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steps:
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sudo apt update
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sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
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python -m pip install --upgrade pip
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pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
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pip install -r requirements/requirements_dev.txt
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pip install uv
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uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
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uv pip install --system -r requirements/requirements_dev.txt
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- name: Debug typing environment
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run: |
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python --version
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mypy --version
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pip freeze | grep -E '^(mypy|types-)'
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mypy --install-types --non-interactive --follow-imports=skip \
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mypy --install-types --non-interactive --follow-imports=skip --ignore-missing-imports \
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tiatoolbox/__init__.py \
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tiatoolbox/__main__.py \
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tiatoolbox/type_hints.py \

‎.github/workflows/pip-install.yml‎

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matrix:
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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python-version: ["3.11", "3.12", "3.13", "3.14"]
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os: [ubuntu-24.04, windows-latest, macos-latest]
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# Force UTF-8 everywhere (Windows is the one that really needs it)
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- name: Checkout
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with:
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fetch-depth: 0
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- name: Install Miniconda
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conda create -y -n test-env python=${{ matrix.python-version }}
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conda create -y -n test-env python=${{ matrix.python-version }} pip
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conda activate test-env
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conda install -y openjpeg sqlite
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python -m pip install --upgrade pip setuptools wheel
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conda create -y -n test-env python=${{ matrix.python-version }}
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conda create -y -n test-env python=${{ matrix.python-version }} pip
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conda activate test-env
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conda install -y openjpeg sqlite
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python -m pip install --upgrade pip setuptools wheel
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source $CONDA/etc/profile.d/conda.sh
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conda activate test-env
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pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
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pip install uv
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uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
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- name: Install CPU-only PyTorch (Windows)
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if: runner.os == 'Windows'
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shell: pwsh
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conda activate test-env
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pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
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pip install uv
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uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
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# (Windows only) make console UTF-8 (extra safety)
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source $CONDA/etc/profile.d/conda.sh
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conda activate test-env
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pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@${GITHUB_SHA}
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pip install uv
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if [[ "${GITHUB_EVENT_NAME}" == "pull_request" ]]; then
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REF="${{ github.event.pull_request.head.sha }}"
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else
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REF="${GITHUB_SHA}"
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fi
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echo "Installing tiatoolbox at ref: $REF"
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uv pip install --system git+https://github.com/TissueImageAnalytics/tiatoolbox@$REF
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- name: Install tiatoolbox (Windows)
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if: runner.os == 'Windows'
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run: |
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conda activate test-env
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pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@$env:GITHUB_SHA
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pip install uv
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uv pip install --system git+https://github.com/TissueImageAnalytics/tiatoolbox@$env:GITHUB_SHA
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# -------------------------------
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# Test Imports

‎.github/workflows/python-package.yml‎

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strategy:
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matrix:
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python-version: ["3.10", "3.11", "3.12", "3.13"]
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python-version: ["3.11", "3.12", "3.13", "3.14"]
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- uses: actions/checkout@v4
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sudo apt update
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sudo apt-get install -y libopenjp2-7 libopenjp2-tools
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python -m pip install --upgrade pip
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python -m pip install ruff==0.15.4 pytest pytest-cov pytest-runner
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pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
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pip install -r requirements/requirements.txt
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python -m pip install ruff==0.15.12 pytest pytest-cov pytest-runner
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pip install uv
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uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
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uv pip install --system -r requirements/requirements.txt
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- uses: actions/checkout@v4
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- name: Set up Python 3.10
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- name: Set up Python 3.11
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uses: actions/setup-python@v4
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with:
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python-version: '3.10'
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python-version: '3.11'
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cache: 'pip'
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sudo apt-get install -y libopenslide-dev libopenjp2-7
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python -m pip install --upgrade pip
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pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
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pip install -r requirements/requirements.txt
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pip install build
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pip install uv
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uv pip install --system torch torchvision --index-url https://download.pytorch.org/whl/cpu
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uv pip install --system -r requirements/requirements.txt
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uv pip install --system build
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- name: Build package
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‎.pre-commit-config.yaml‎

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- id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
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- repo: https://github.com/astral-sh/ruff-pre-commit
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# Ruff version.
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rev: v0.15.4
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rev: v0.15.12
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hooks:
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- id: ruff
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args: [--fix, --exit-non-zero-on-fix]

‎AUTHORS.md‎

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- Abishekraj Vinayagar Gnanasambandam \<@AbishekRajVG>
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- Wenqi Lu \<@wenqi006>
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- Saad Bashir \<@rajasaad>
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- Aakash Madhav Rao \<@mraoaakash>
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- Behnaz Elhaminia \<@behnazelhaminia>
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## Contributors

‎CITATION.cff‎

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given-names: "Shan E Ahmed"
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orcid: "https://orcid.org/0000-0002-1097-1738"
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title: "TIAToolbox as an end-to-end library for advanced tissue image analytics"
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version: 2.0.1 # TIAToolbox version
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version: 2.1.0 # TIAToolbox version
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doi: 10.5281/zenodo.5802442
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date-released: 2022-10-20
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url: "https://github.com/TissueImageAnalytics/tiatoolbox"

‎CONTRIBUTING.rst‎

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1. The pull request should include tests.
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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.
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3. The pull request should work for Python 3.10, 3.11, 3.12 and 3.13, 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.
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3. The pull request should work for all Python versions supported by the project (including CPython and PyPy). Check https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml and make sure that the tests pass for all supported Python versions.
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Tips
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----

‎HISTORY.md‎

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# History
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## TIAToolbox v2.1.0 (2026-05-19)
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5+
### ✨ Major Updates and Feature Improvements
6+
7+
- Python ≥3.11 required
8+
- Supports up to 3.14 (#1035)
9+
- Drops support for 3.10 (#1034)
10+
- Zarr v3 Support (#904)
11+
- New storage APIs (zarr.Array, LocalStore, FsspecStore)
12+
- Removal of object arrays → rectangular storage via pad_contours
13+
- Update `FsspecJsonWSIReader` to support Zarr v3 (#1049), thanks to @aacic
14+
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### ⚠️ API Changes
16+
17+
- Python requirement updated → >=3.11, \<3.15
18+
19+
### 🐞 Bug Fixes and Other Changes
20+
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- Fixed
22+
- Contour serialization and padding issues (Zarr compatibility) (#904)
23+
- Invalid Geometry in JSON Outputs (#1057)
24+
- Fix typographical errors in `pre-trained` documentation (#1043, #1062)
25+
26+
### 🛠️ Development-Related Changes
27+
28+
- Use `uv` to set up CI environments, reduces installation time
29+
- Update instructions for `uv` install
30+
- Use `max_image` for `remove_small_objects` in `scikit-image` usage (#1048)
31+
- Improve `mypy` workflow and typing errors (#1045)
32+
33+
______________________________________________________________________
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## TIAToolbox v2.0.1 (2026-03-16)
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### Bug Fixes and Other Changes

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