careamics 0.0.15__tar.gz → 0.0.17__tar.gz

{careamics-0.0.15 → careamics-0.0.17}/.github/dependabot.yml

@@ -7,5 +7,5 @@ updates:
       interval: "daily"
       time: "08:00"
     ignore:
-      - dependency-name: "numpy"
       - dependency-name: "zarr"
+      - dependency-name: "torchmetrics"

careamics-0.0.17/.github/workflows/ci.yml

@@ -0,0 +1,98 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+jobs:
+  check-manifest:
+    # check-manifest is a tool that checks that all files in version control are
+    # included in the sdist (unless explicitly excluded)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - run: pipx run check-manifest
+
+  test:
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+        # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
+        platform: [ubuntu-latest, windows-latest, macos-latest ]
+
+    steps:
+      - name: 🛑 Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          # Install a specific version of uv.
+          version: "0.9.0"
+          enable-cache: true
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: 🧪 Run tests
+        run: uv run pytest --color=yes -m "not lvae"
+
+
+  deploy:
+    name: Release
+    needs: test
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+      # This permission allows writing releases
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          # Install a specific version of uv.
+          version: "0.9.0"
+          enable-cache: true
+          python-version: 3.12
+
+      - name: Build
+        run: uv build
+
+      # Check that basic features work and we didn't miss to include crucial files
+      - name: Smoke test (wheel)
+        run: uv run --isolated --no-project --with dist/*.whl tests/smoke_test.py
+
+      - name: Smoke test (source distribution)
+        run: uv run --isolated --no-project --with dist/*.tar.gz tests/smoke_test.py
+        
+      - name: Publish
+        run: uv publish
+
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true

careamics-0.0.17/.github/workflows/ci_lvae.yml

@@ -0,0 +1,45 @@
+name: CI-lvae-uv
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    # run every week (for --pre release tests)
+    - cron: "0 0 * * 0"
+
+jobs:
+  test:
+    name: LVAE py3.12 (ubuntu-latest)
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - name: 🛑 Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v5
+            
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          # Install a specific version of uv.
+          version: "0.9.0"
+          enable-cache: true
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: 🧪 Run tests
+        # does not run doctests
+        run: uv run pytest tests --color=yes -m lvae

careamics-0.0.17/.github/workflows/codecov.yml

@@ -0,0 +1,43 @@
+name: codecov
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  codecov:
+    name: codecov update
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - name: 🛑 Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          access_token: ${{ github.token }}
+
+      - name: Checkout code
+        uses: actions/checkout@v5
+  
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          # Install a specific version of uv.
+          version: "0.9.0"
+          enable-cache: true
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: 🧪 Run Tests
+        run: uv run pytest --color=yes --cov --cov-config=pyproject.toml --cov-report=xml --cov-report=term-missing 
+
+      - name: Coverage
+        uses: codecov/codecov-action@v5
+        with:
+          version: v0.7.3

{careamics-0.0.15 → careamics-0.0.17}/.pre-commit-config.yaml

@@ -14,26 +14,25 @@ repos:
       - id: validate-pyproject
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.2
+    rev: v0.13.3
     hooks:
       - id: ruff
         exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^scripts/.*"
-        args: [--fix, --target-version, py310]
 
-  - repo: https://github.com/psf/black
-    rev: 25.1.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 25.9.0
     hooks:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.1
+    rev: v1.18.2
     hooks:
       - id: mypy
         files: "^src/"
         exclude: "^src/careamics/lvae_training/.*|^src/careamics/models/lvae/.*|^src/careamics/config/likelihood_model.py|^src/careamics/losses/loss_factory.py|^src/careamics/losses/lvae/losses.py"
         args: ["--config-file", "mypy.ini"]
         additional_dependencies:
-          - numpy<2.0.0
+          - numpy
           - pydantic
           - types-PyYAML
           - types-setuptools

{careamics-0.0.15 → careamics-0.0.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: careamics
-Version: 0.0.15
+Version: 0.0.17
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -10,33 +10,30 @@ License-File: LICENSE
 Classifier: Development Status :: 3 - Alpha
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Typing :: Typed
-Requires-Python: >=3.10
-Requires-Dist: bioimageio-core==0.9.0
-Requires-Dist: matplotlib<=3.10.3
-Requires-Dist: numpy<2.0.0
-Requires-Dist: pillow<=11.2.1
-Requires-Dist: psutil<=7.0.0
-Requires-Dist: pydantic<=2.12,>=2.11
-Requires-Dist: pytorch-lightning<=2.5.2,>=2.2
-Requires-Dist: pyyaml!=6.0.0,<=6.0.2
+Requires-Python: >=3.11
+Requires-Dist: bioimageio-core>=0.9.0
+Requires-Dist: matplotlib<=3.10.7
+Requires-Dist: numpy>=1.21
+Requires-Dist: numpy>=2.1.0; python_version >= '3.13'
+Requires-Dist: pillow<=11.3.0
+Requires-Dist: psutil<=7.1.0
+Requires-Dist: pydantic<=2.12.2,>=2.11
+Requires-Dist: pytorch-lightning<=2.5.5,>=2.2
+Requires-Dist: pyyaml!=6.0.0,<=6.0.3
 Requires-Dist: scikit-image<=0.25.2
-Requires-Dist: tifffile<=2025.5.10
-Requires-Dist: torch<=2.7.1,>=2.0
-Requires-Dist: torchvision<=0.22.1
-Requires-Dist: typer<=0.16.0,>=0.12.3
-Requires-Dist: zarr<3.0.0
+Requires-Dist: tifffile<=2025.10.4
+Requires-Dist: torch<=2.8.0,>=2.0
+Requires-Dist: torchmetrics<1.5.0,>=0.11.0
+Requires-Dist: torchvision<=0.23.0
+Requires-Dist: typer<=0.19.2,>=0.12.3
+Requires-Dist: validators<=0.35.0
+Requires-Dist: zarr<4.0.0,>=3.0.0
 Provides-Extra: czi
 Requires-Dist: pylibczirw<6.0.0,>=4.1.2; extra == 'czi'
-Provides-Extra: dev
-Requires-Dist: onnx; extra == 'dev'
-Requires-Dist: pre-commit; extra == 'dev'
-Requires-Dist: pytest; extra == 'dev'
-Requires-Dist: pytest-cov; extra == 'dev'
-Requires-Dist: sybil; extra == 'dev'
 Provides-Extra: examples
 Requires-Dist: careamics-portfolio; extra == 'examples'
 Requires-Dist: jupyter; extra == 'examples'

{careamics-0.0.15 → careamics-0.0.17}/pyproject.toml

@@ -20,7 +20,7 @@ name = "careamics"
 dynamic = ["version"]
 description = "Toolbox for running N2V and friends."
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 license = { text = "BSD-3-Clause" }
 authors = [
     { name = 'CAREamics team', email = 'rse@fht.org' },
@@ -34,27 +34,30 @@ authors = [
 classifiers = [
     "Development Status :: 3 - Alpha",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "License :: OSI Approved :: BSD License",
     "Typing :: Typed",
 ]
 dependencies = [
-    'numpy<2.0.0',
-    'torch>=2.0,<=2.7.1',
-    'torchvision<=0.22.1',
-    'bioimageio.core==0.9.0',
-    'tifffile<=2025.5.10',
-    'psutil<=7.0.0',
-    'pydantic>=2.11,<=2.12',
-    'pytorch_lightning>=2.2,<=2.5.2',
-    'pyyaml<=6.0.2,!=6.0.0',
-    'typer>=0.12.3,<=0.16.0',
+    "numpy>=1.21",
+    "numpy>=2.1.0; python_version>='3.13'", # prevents ml_dtypes conflict in py313
+    'torch>=2.0,<=2.8.0',
+    'torchvision<=0.23.0',
+    'bioimageio.core>=0.9.0',
+    'tifffile<=2025.10.4',
+    'psutil<=7.1.0',
+    'pydantic>=2.11,<=2.12.2',
+    'pytorch_lightning>=2.2,<=2.5.5',
+    'pyyaml!=6.0.0,<=6.0.3',
+    'typer>=0.12.3,<=0.19.2',
     'scikit-image<=0.25.2',
-    'zarr<3.0.0',
-    'pillow<=11.2.1',
-    'matplotlib<=3.10.3',
+    'zarr>=3.0.0,<4.0.0',
+    'pillow<=11.3.0',
+    'matplotlib<=3.10.7',
+    'validators<=0.35.0',
+    'torchmetrics>=0.11.0,<1.5.0' # 1.5.0 causes `data_range` mandatory parameter issues
 ]
 
 [project.optional-dependencies]
@@ -62,21 +65,25 @@ dependencies = [
 # czi format
 czi = ['pylibCZIrw>=4.1.2,<6.0.0']
 
+# notebooks
+examples = ["jupyter", "careamics-portfolio"]
+
+# loggers
+wandb = ["wandb"]
+tensorboard = ["tensorboard", "protobuf==5.29.1"]
+
+[dependency-groups]
 # development dependencies and tooling
 dev = [
     "pre-commit",
     "pytest",
     "pytest-cov",
-    "onnx",
     "sybil",      # doctesting
-]
 
-# notebooks
-examples = ["jupyter", "careamics-portfolio"]
-
-# loggers
-wandb = ["wandb"]
-tensorboard = ["tensorboard", "protobuf==5.29.1"]
+    # libraries used in some tests
+    "onnx",
+    "ml_dtypes>=0.5.0" # required by onnx, causes issues in gh runners with py313
+]
 
 [project.urls]
 homepage = "https://careamics.github.io/"
@@ -88,8 +95,9 @@ careamics = "careamics.cli.main:run"
 
 # https://beta.ruff.rs/docs
 [tool.ruff]
+fix = true
 line-length = 88
-target-version = "py310"
+target-version = "py311" # is this needed? see .pre-commit-config.yaml
 src = ["src"]
 lint.select = [
     "E",  # style errors

{careamics-0.0.15 → careamics-0.0.17}/src/careamics/careamist.py

@@ -41,6 +41,7 @@ logger = get_logger(__name__)
 LOGGER_TYPES = list[Union[TensorBoardLogger, WandbLogger, CSVLogger]]
 
 
+# TODO type ignore have been added because of the czi data type in data configuration
 class CAREamist:
     """Main CAREamics class, allowing training and prediction using various algorithms.
 
@@ -208,17 +209,11 @@ class CAREamist:
 
         # instantiate trainer
         self.trainer = Trainer(
-            max_epochs=self.cfg.training_config.num_epochs,
-            precision=self.cfg.training_config.precision,
-            max_steps=self.cfg.training_config.max_steps,
-            check_val_every_n_epoch=self.cfg.training_config.check_val_every_n_epoch,
             enable_progress_bar=enable_progress_bar,
-            accumulate_grad_batches=self.cfg.training_config.accumulate_grad_batches,
-            gradient_clip_val=self.cfg.training_config.gradient_clip_val,
-            gradient_clip_algorithm=self.cfg.training_config.gradient_clip_algorithm,
             callbacks=self.callbacks,
             default_root_dir=self.work_dir,
             logger=experiment_logger,
+            **self.cfg.training_config.lightning_trainer_config or {},
         )
 
         # place holder for the datamodules
@@ -264,7 +259,7 @@ class CAREamist:
                 HyperParametersCallback(self.cfg),
                 ModelCheckpoint(
                     dirpath=self.work_dir / Path("checkpoints"),
-                    filename=self.cfg.experiment_name,
+                    filename=f"{self.cfg.experiment_name}_{{epoch:02d}}_step_{{step}}",
                     **self.cfg.training_config.checkpoint_callback.model_dump(),
                 ),
             ]
@@ -680,7 +675,7 @@ class CAREamist:
         # create the prediction
         self.pred_datamodule = create_predict_datamodule(
             pred_data=source,
-            data_type=data_type or self.cfg.data_config.data_type,
+            data_type=data_type or self.cfg.data_config.data_type,  # type: ignore
             axes=axes or self.cfg.data_config.axes,
             image_means=self.cfg.data_config.image_means,
             image_stds=self.cfg.data_config.image_stds,
@@ -826,11 +821,13 @@ class CAREamist:
         source_data_type: Literal["array", "tiff", "custom"]
         if isinstance(source, PredictDataModule):
             source_path = source.pred_data
-            source_data_type = source.data_type
+            source_data_type = source.data_type  # type: ignore
             extension_filter = source.extension_filter
-        elif isinstance(source, str | Path):
+        elif isinstance(source, (str | Path)):
             source_path = source
-            source_data_type = data_type or self.cfg.data_config.data_type
+            source_data_type = (
+                data_type or self.cfg.data_config.data_type  # type: ignore
+            )
             extension_filter = SupportedData.get_extension_pattern(
                 SupportedData(source_data_type)
             )
@@ -841,7 +838,7 @@ class CAREamist:
             raise ValueError(
                 "Predicting to disk is not supported for input type 'array'."
             )
-        assert isinstance(source_path, str | Path)  # because data_type != "array"
+        assert isinstance(source_path, (Path | str))  # because data_type != "array"
         source_path = Path(source_path)
 
         file_paths = list_files(source_path, source_data_type, extension_filter)
@@ -879,7 +876,7 @@ class CAREamist:
 
     def export_to_bmz(
         self,
-        path_to_archive: Union[Path, str],
+        path_to_archive: Union[Path | str],
         friendly_model_name: str,
         input_array: NDArray,
         authors: list[dict],

{careamics-0.0.15 → careamics-0.0.17}/src/careamics/cli/conf.py

@@ -116,7 +116,11 @@ def care(  # numpydoc ignore=PR01
         ),
     ],
     batch_size: Annotated[int, typer.Option(help="Batch size.")],
-    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")],
+    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")] = 100,
+    num_steps: Annotated[
+        int | None,
+        typer.Option(help="Number of batches per epoch (limit_train_batches)."),
+    ] = None,
     data_type: Annotated[
         click.Choice,
         typer.Option(click_type=click.Choice(["tiff"]), help="Type of the data."),
@@ -175,6 +179,7 @@ def care(  # numpydoc ignore=PR01
         patch_size=patch_size,
         batch_size=batch_size,
         num_epochs=num_epochs,
+        num_steps=num_steps,
         # TODO: fix choosing augmentations
         augmentations=None if use_augmentations else [],
         independent_channels=independent_channels,
@@ -203,7 +208,11 @@ def n2n(  # numpydoc ignore=PR01
         ),
     ],
     batch_size: Annotated[int, typer.Option(help="Batch size.")],
-    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")],
+    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")] = 100,
+    num_steps: Annotated[
+        int | None,
+        typer.Option(help="Number of batches per epoch (limit_train_batches)."),
+    ] = None,
     data_type: Annotated[
         click.Choice,
         typer.Option(click_type=click.Choice(["tiff"]), help="Type of the data."),
@@ -259,6 +268,7 @@ def n2n(  # numpydoc ignore=PR01
         patch_size=patch_size,
         batch_size=batch_size,
         num_epochs=num_epochs,
+        num_steps=num_steps,
         # TODO: fix choosing augmentations
         augmentations=None if use_augmentations else [],
         independent_channels=independent_channels,
@@ -287,7 +297,11 @@ def n2v(  # numpydoc ignore=PR01
         ),
     ],
     batch_size: Annotated[int, typer.Option(help="Batch size.")],
-    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")],
+    num_epochs: Annotated[int, typer.Option(help="Number of epochs.")] = 100,
+    num_steps: Annotated[
+        int | None,
+        typer.Option(help="Number of batches per epoch (limit_train_batches)."),
+    ] = None,
     data_type: Annotated[
         click.Choice,
         typer.Option(click_type=click.Choice(["tiff"]), help="Type of the data."),
@@ -364,6 +378,7 @@ def n2v(  # numpydoc ignore=PR01
         patch_size=patch_size,
         batch_size=batch_size,
         num_epochs=num_epochs,
+        num_steps=num_steps,
         # TODO: fix choosing augmentations
         augmentations=None if use_augmentations else [],
         independent_channels=independent_channels,

{careamics-0.0.15 → careamics-0.0.17}/src/careamics/config/__init__.py

@@ -12,8 +12,10 @@ __all__ = [
     "Configuration",
     "DataConfig",
     "GaussianMixtureNMConfig",
+    "HDNAlgorithm",
     "InferenceConfig",
     "LVAELossConfig",
+    "MicroSplitAlgorithm",
     "MultiChannelNMConfig",
     "N2NAlgorithm",
     "N2VAlgorithm",
@@ -22,6 +24,8 @@ __all__ = [
     "VAEBasedAlgorithm",
     "algorithm_factory",
     "create_care_configuration",
+    "create_hdn_configuration",
+    "create_microsplit_configuration",
     "create_n2n_configuration",
     "create_n2v_configuration",
     "load_configuration",
@@ -30,6 +34,8 @@ __all__ = [
 
 from .algorithms import (
     CAREAlgorithm,
+    HDNAlgorithm,
+    MicroSplitAlgorithm,
     N2NAlgorithm,
     N2VAlgorithm,
     UNetBasedAlgorithm,
@@ -40,6 +46,8 @@ from .configuration import Configuration
 from .configuration_factories import (
     algorithm_factory,
     create_care_configuration,
+    create_hdn_configuration,
+    create_microsplit_configuration,
     create_n2n_configuration,
     create_n2v_configuration,
 )

{careamics-0.0.15 → careamics-0.0.17}/src/careamics/config/algorithms/__init__.py

@@ -2,6 +2,8 @@
 
 __all__ = [
     "CAREAlgorithm",
+    "HDNAlgorithm",
+    "MicroSplitAlgorithm",
     "N2NAlgorithm",
     "N2VAlgorithm",
     "UNetBasedAlgorithm",
@@ -9,6 +11,8 @@ __all__ = [
 ]
 
 from .care_algorithm_model import CAREAlgorithm
+from .hdn_algorithm_model import HDNAlgorithm
+from .microsplit_algorithm_model import MicroSplitAlgorithm
 from .n2n_algorithm_model import N2NAlgorithm
 from .n2v_algorithm_model import N2VAlgorithm
 from .unet_algorithm_model import UNetBasedAlgorithm

careamics-0.0.17/src/careamics/config/algorithms/hdn_algorithm_model.py

@@ -0,0 +1,103 @@
+"""HDN algorithm configuration."""
+
+from typing import Literal
+
+from bioimageio.spec.generic.v0_3 import CiteEntry
+from pydantic import ConfigDict
+
+from careamics.config.algorithms.vae_algorithm_model import VAEBasedAlgorithm
+from careamics.config.architectures import LVAEModel
+from careamics.config.loss_model import LVAELossConfig
+
+HDN = "Hierarchical DivNoising"
+
+HDN_DESCRIPTION = (
+    "HDN leverages a hierarchical VAE to perform image "
+    "restoration. It is designed to be interpretable and unsupervised, "
+    "making it suitable for a wide range of microscopy images."
+)
+HDN_REF = CiteEntry(
+    text='Prakash, M., Delbracio, M., Milanfar, P., Jug, F. 2022. "Interpretable '
+    'Unsupervised Diversity Denoising and Artefact Removal." The International '
+    "Conference on Learning Representations (ICLR).",
+    doi="10.1561/2200000056",
+)
+
+
+class HDNAlgorithm(VAEBasedAlgorithm):
+    """HDN algorithm configuration."""
+
+    model_config = ConfigDict(validate_assignment=True)
+
+    algorithm: Literal["hdn"] = "hdn"
+
+    loss: LVAELossConfig
+
+    model: LVAEModel  # TODO add validators
+
+    is_supervised: bool = False
+
+    def get_algorithm_friendly_name(self) -> str:
+        """
+        Get the algorithm friendly name.
+
+        Returns
+        -------
+        str
+            Friendly name of the algorithm.
+        """
+        return HDN
+
+    def get_algorithm_keywords(self) -> list[str]:
+        """
+        Get algorithm keywords.
+
+        Returns
+        -------
+        list[str]
+            List of keywords.
+        """
+        return [
+            "restoration",
+            "VAE",
+            "3D" if self.model.is_3D() else "2D",
+            "CAREamics",
+            "pytorch",
+        ]
+
+    def get_algorithm_references(self) -> str:
+        """
+        Get the algorithm references.
+
+        This is used to generate the README of the BioImage Model Zoo export.
+
+        Returns
+        -------
+        str
+            Algorithm references.
+        """
+        return HDN_REF.text + " doi: " + HDN_REF.doi
+
+    def get_algorithm_citations(self) -> list[CiteEntry]:
+        """
+        Return a list of citation entries of the current algorithm.
+
+        This is used to generate the model description for the BioImage Model Zoo.
+
+        Returns
+        -------
+        List[CiteEntry]
+            List of citation entries.
+        """
+        return [HDN_REF]
+
+    def get_algorithm_description(self) -> str:
+        """
+        Get the algorithm description.
+
+        Returns
+        -------
+        str
+            Algorithm description.
+        """
+        return HDN_DESCRIPTION