diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 31de2a1..b9039eb 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -10,7 +10,7 @@ on:
     branches: ["main"]
 
 jobs:
-  build:
+  test:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -32,7 +32,7 @@ jobs:
           python -m pip install poetry
       - name: Install dependencies
         run: |
-          python -m poetry install
+          python -m poetry install --extras test
       - name: Test with pytest and create coverage report
         run: |
           python -m poetry run coverage run --source=panoptica -m pytest
@@ -43,3 +43,35 @@ jobs:
         uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
+
+  test-cuda:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+
+      - name: Configure poetry
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install poetry
+      - name: Install dependencies with GPU extras
+        run: |
+          python -m poetry install --extras "gpu test" || python -m poetry install --extras test
+      - name: Test CUDA functionality (CPU fallback)
+        run: |
+          python -m poetry run pytest unit_tests/test_cupy_connected_components.py -v
+      - name: Upload coverage results to Codecov (Only on merge to main)
+        # Only upload to Codecov after a merge to the main branch
+        if: github.ref == 'refs/heads/main' && github.event_name == 'push'
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/benchmark/benchmark.py b/benchmark/benchmark.py
index c9a370c..a2740af 100644
--- a/benchmark/benchmark.py
+++ b/benchmark/benchmark.py
@@ -7,6 +7,16 @@
 # scipy needs to be installed to run this benchmark, we use cc3d as it is quicker for 3D data
 from scipy import ndimage
 
+# Try to import cupy for GPU acceleration
+try:
+    import cupy as cp
+    from cupyx.scipy import ndimage as cp_ndimage
+
+    CUPY_AVAILABLE = True
+except ImportError:
+    CUPY_AVAILABLE = False
+    print("CuPy not available. GPU benchmarks will be skipped.")
+
 
 def generate_random_binary_mask(size: Tuple[int, int, Union[int, None]]) -> np.ndarray:
     """
@@ -64,6 +74,64 @@ def label_cc3d():
     return cc3d_time
 
 
+def benchmark_cupy(mask: np.ndarray):
+    """
+    Benchmark the performance of cupy.ndimage.label for connected component labeling on GPU.
+
+    Args:
+        mask (np.ndarray): Binary mask to label.
+
+    Returns:
+        float: Time taken to label the mask in seconds, or None if CuPy is not available.
+    """
+    if not CUPY_AVAILABLE:
+        return None
+
+    # Transfer data to GPU
+    mask_gpu = cp.asarray(mask)
+
+    # Warmup phase
+    for _ in range(3):
+        cp_ndimage.label(mask_gpu)
+        cp.cuda.Stream.null.synchronize()
+
+    def label_cupy():
+        cp_ndimage.label(mask_gpu)
+        cp.cuda.Stream.null.synchronize()  # Ensure GPU computation is complete
+
+    cupy_time = timeit.timeit(label_cupy, number=10)
+
+    # Clean up GPU memory
+    del mask_gpu
+    cp.get_default_memory_pool().free_all_blocks()
+
+    return cupy_time
+
+
+def benchmark_panoptica_cupy(mask: np.ndarray):
+    """
+    Benchmark the performance of panoptica's CuPy backend for connected component labeling.
+
+    Args:
+        mask (np.ndarray): Binary mask to label.
+
+    Returns:
+        float: Time taken to label the mask in seconds, or None if CuPy is not available.
+    """
+    if not CUPY_AVAILABLE:
+        return None
+
+    from panoptica._functionals import _connected_components
+    from panoptica.utils.constants import CCABackend
+
+    def label_panoptica_cupy():
+        _connected_components(mask, CCABackend.cupy)
+
+    panoptica_cupy_time = timeit.timeit(label_panoptica_cupy, number=10)
+
+    return panoptica_cupy_time
+
+
 def run_benchmarks(volume_sizes: Tuple[Tuple[int, int, Union[int, None]]]) -> None:
     """
     Run benchmark tests for connected component labeling with different volume sizes.
@@ -80,10 +148,15 @@ def run_benchmarks(volume_sizes: Tuple[Tuple[int, int, Union[int, None]]]) -> No
 
         scipy_time = benchmark_scipy(mask)
         cc3d_time = benchmark_cc3d(mask)
+        cupy_time = benchmark_cupy(mask)
 
         print(f"Volume Size: {size}")
         print(f"Scipy Time: {scipy_time:.4f} seconds")
         print(f"CC3D Time: {cc3d_time:.4f} seconds")
+        if cupy_time is not None:
+            print(f"CuPy Time: {cupy_time:.4f} seconds")
+        else:
+            print("CuPy Time: Not available")
         print()
 
 
diff --git a/panoptica/__init__.py b/panoptica/__init__.py
index feb7387..4a43a37 100644
--- a/panoptica/__init__.py
+++ b/panoptica/__init__.py
@@ -2,7 +2,11 @@
     ConnectedComponentsInstanceApproximator,
     CCABackend,
 )
-from panoptica.instance_matcher import NaiveThresholdMatching, MaxBipartiteMatching
+from panoptica.instance_matcher import (
+    NaiveThresholdMatching,
+    MaxBipartiteMatching,
+    RegionBasedMatching,
+)
 from panoptica.panoptica_statistics import Panoptica_Statistic, ValueSummary
 from panoptica.panoptica_aggregator import Panoptica_Aggregator
 from panoptica.panoptica_evaluator import Panoptica_Evaluator
diff --git a/panoptica/_functionals.py b/panoptica/_functionals.py
index 98e4345..7168be7 100644
--- a/panoptica/_functionals.py
+++ b/panoptica/_functionals.py
@@ -63,6 +63,19 @@ def _connected_components(
         from scipy.ndimage import label
 
         cc_arr, n_instances = label(array)
+    elif cca_backend == CCABackend.cupy:
+        try:
+            import cupy as cp
+            from cupyx.scipy.ndimage import label as cp_label
+
+            array_gpu = cp.asarray(array)
+            cc_arr, n_instances = cp_label(array_gpu)
+            cc_arr = cp.asnumpy(cc_arr)
+        except ImportError:
+            raise ImportError(
+                "CuPy is not installed. Please install CuPy to use the GPU backend. "
+                "You can install it using: pip install cupy-cuda11x or cupy-cuda12x depending on your CUDA version."
+            )
     else:
         raise NotImplementedError(cca_backend)
 
diff --git a/panoptica/instance_matcher.py b/panoptica/instance_matcher.py
index f52e9ba..0eb4afc 100644
--- a/panoptica/instance_matcher.py
+++ b/panoptica/instance_matcher.py
@@ -3,11 +3,13 @@
 from typing import Optional, Tuple, List
 
 import numpy as np
+from scipy.ndimage import distance_transform_edt
 
 from panoptica._functionals import (
     _calc_matching_metric_of_overlapping_labels,
     _calc_matching_metric_of_overlapping_partlabels,
     _map_labels,
+    _connected_components,
 )
 from panoptica.metrics import Metric
 from panoptica.utils.processing_pair import (
@@ -17,6 +19,7 @@
 from panoptica.utils.instancelabelmap import InstanceLabelMap
 from panoptica.utils.config import SupportsConfig
 from panoptica.utils.label_group import LabelGroup, LabelPartGroup
+from panoptica.utils.constants import CCABackend
 
 
 @dataclass
@@ -493,3 +496,118 @@ def _yaml_repr(cls, node) -> dict:
             "matching_metric": node._matching_metric,
             "matching_threshold": node._matching_threshold,
         }
+
+
+class RegionBasedMatching(InstanceMatchingAlgorithm):
+    """
+    Instance matching algorithm that performs region-based matching using spatial distance.
+
+    This method assigns prediction instances to ground truth regions based on spatial proximity
+    rather than traditional overlap-based metrics. It uses connected components and distance
+    transforms to create region assignments.
+
+    Note: This matching method does not produce traditional count metrics (TP/FP/FN) as it
+    assigns all predictions to regions. Count metrics will be set to NaN.
+
+    Attributes:
+        cca_backend (CCABackend): Backend for connected component analysis.
+    """
+
+    def __init__(
+        self,
+        cca_backend: CCABackend = CCABackend.scipy,
+    ) -> None:
+        """
+        Initialize the RegionBasedMatching instance.
+
+        Args:
+            cca_backend (CCABackend): Backend for connected component analysis.
+        """
+        self._cca_backend = cca_backend
+
+    def _get_gt_regions(self, gt: np.ndarray) -> Tuple[np.ndarray, int]:
+        """
+        Get ground truth regions using connected components and distance transforms.
+
+        Args:
+            gt: Ground truth array
+
+        Returns:
+            Tuple of (region_map, num_features) where region_map assigns each pixel
+            to the closest ground truth region.
+        """
+        # Step 1: Connected Components
+        labeled_array, num_features = _connected_components(gt, self._cca_backend)
+
+        # Step 2: Compute distance transform for each region
+        distance_map = np.full(gt.shape, np.inf, dtype=np.float32)
+        region_map = np.zeros(gt.shape, dtype=np.int32)
+
+        for region_label in range(1, num_features + 1):
+            # Create region mask
+            region_mask = labeled_array == region_label
+
+            # Compute distance transform
+            distance = distance_transform_edt(~region_mask)
+
+            # Update pixels where this region is closer
+            update_mask = distance < distance_map
+            distance_map[update_mask] = distance[update_mask]
+            region_map[update_mask] = region_label
+
+        return region_map, num_features
+
+    def _match_instances(
+        self,
+        unmatched_instance_pair: UnmatchedInstancePair,
+        context: Optional[MatchingContext] = None,
+        **kwargs,
+    ) -> InstanceLabelMap:
+        """
+        Perform region-based instance matching.
+
+        Args:
+            unmatched_instance_pair (UnmatchedInstancePair): The unmatched instance pair to be matched.
+            context (Optional[MatchingContext]): The matching context.
+            **kwargs: Additional keyword arguments.
+
+        Returns:
+            InstanceLabelMap: The result of the region-based matching.
+        """
+        pred_arr = unmatched_instance_pair.prediction_arr
+        ref_arr = unmatched_instance_pair.reference_arr
+        pred_labels = unmatched_instance_pair.pred_labels
+
+        labelmap = InstanceLabelMap()
+
+        if len(pred_labels) == 0:
+            return labelmap
+
+        # Get ground truth regions
+        region_map, num_features = self._get_gt_regions(ref_arr)
+
+        # For each prediction instance, find which ground truth region it belongs to
+        for pred_label in pred_labels:
+            pred_mask = pred_arr == pred_label
+
+            # Find the most common region assignment for this prediction instance
+            pred_regions = region_map[pred_mask]
+
+            # Remove background (region 0)
+            pred_regions = pred_regions[pred_regions > 0]
+
+            if len(pred_regions) > 0:
+                # Assign to the most common region
+                unique_regions, counts = np.unique(pred_regions, return_counts=True)
+                most_common_region = unique_regions[np.argmax(counts)]
+
+                # Add to labelmap
+                labelmap.add_labelmap_entry(int(pred_label), int(most_common_region))
+
+        return labelmap
+
+    @classmethod
+    def _yaml_repr(cls, node) -> dict:
+        return {
+            "cca_backend": node._cca_backend,
+        }
diff --git a/panoptica/panoptica_evaluator.py b/panoptica/panoptica_evaluator.py
index db6ec17..6b2e2cf 100644
--- a/panoptica/panoptica_evaluator.py
+++ b/panoptica/panoptica_evaluator.py
@@ -442,6 +442,11 @@ def panoptic_evaluate(
             else instance_metadata["original_num_refs"]
         )
 
+        # For region-based matching, set TP to NaN since it doesn't use traditional counting
+        tp_value = processing_pair.tp
+        if instance_matcher.__class__.__name__ == "RegionBasedMatching":
+            tp_value = np.nan
+
         processing_pair = PanopticaResult(
             reference_arr=processing_pair.reference_arr,
             prediction_arr=processing_pair.prediction_arr,
@@ -450,7 +455,7 @@ def panoptic_evaluate(
             num_ref_instances=final_num_ref_instances,
             num_ref_labels=instance_metadata["num_ref_labels"],
             label_group=label_group,
-            tp=processing_pair.tp,
+            tp=tp_value,
             list_metrics=processing_pair.list_metrics,
             global_metrics=global_metrics,
             edge_case_handler=edge_case_handler,
diff --git a/panoptica/panoptica_result.py b/panoptica/panoptica_result.py
index f0cd6c0..aaaf560 100644
--- a/panoptica/panoptica_result.py
+++ b/panoptica/panoptica_result.py
@@ -25,7 +25,7 @@ def __init__(
         prediction_arr: np.ndarray,
         num_pred_instances: int,
         num_ref_instances: int,
-        tp: int,
+        tp: int | float,  # Allow NaN (float) for region-based matching
         list_metrics: dict[Metric, list[float]],
         edge_case_handler: EdgeCaseHandler,
         global_metrics: list[Metric] = [],
@@ -96,7 +96,7 @@ def __init__(
             default_value=num_pred_instances,
             was_calculated=True,
         )
-        self.tp: int
+        self.tp: int | float  # Allow NaN for region-based matching
         self._add_metric(
             "tp",
             MetricType.MATCHING,
@@ -108,28 +108,28 @@ def __init__(
         # endregion
         #
         # region Basic
-        self.fp: int
+        self.fp: int | float  # Allow NaN for region-based matching
         self._add_metric(
             "fp",
             MetricType.MATCHING,
             fp,
             long_name="False Positives",
         )
-        self.fn: int
+        self.fn: int | float  # Allow NaN for region-based matching
         self._add_metric(
             "fn",
             MetricType.MATCHING,
             fn,
             long_name="False Negatives",
         )
-        self.prec: int
+        self.prec: int | float  # Allow NaN for region-based matching
         self._add_metric(
             "prec",
             MetricType.NO_PRINT,
             prec,
             long_name="Precision (positive predictive value)",
         )
-        self.rec: int
+        self.rec: int | float  # Allow NaN for region-based matching
         self._add_metric(
             "rec",
             MetricType.NO_PRINT,
@@ -773,18 +773,26 @@ def get_channel_metrics(self, metric_name: str):
 
 # region Basic
 def fp(res: PanopticaResult):
+    if np.isnan(res.tp):
+        return np.nan
     return res.num_pred_instances - res.tp
 
 
 def fn(res: PanopticaResult):
+    if np.isnan(res.tp):
+        return np.nan
     return res.num_ref_instances - res.tp
 
 
 def prec(res: PanopticaResult):
+    if np.isnan(res.tp):
+        return np.nan
     return res.tp / (res.tp + res.fp)
 
 
 def rec(res: PanopticaResult):
+    if np.isnan(res.tp):
+        return np.nan
     return res.tp / (res.tp + res.fn)
 
 
@@ -795,6 +803,8 @@ def rq(res: PanopticaResult):
     Returns:
         float: Recognition Quality (RQ).
     """
+    if np.isnan(res.tp):
+        return np.nan
     if res.tp == 0:
         return 0.0 if res.num_pred_instances + res.num_ref_instances > 0 else np.nan
     return res.tp / (res.tp + 0.5 * res.fp + 0.5 * res.fn)
diff --git a/panoptica/utils/constants.py b/panoptica/utils/constants.py
index 7dc88a0..463fad0 100644
--- a/panoptica/utils/constants.py
+++ b/panoptica/utils/constants.py
@@ -89,10 +89,13 @@ class CCABackend(_Enum_Compare):
           [CC3D Website](https://github.com/seung-lab/connected-components-3d)
         - scipy: Represents the SciPy backend for CCA.
           [SciPy Website](https://www.scipy.org/)
+        - cupy: Represents the CuPy backend for GPU-accelerated CCA.
+          [CuPy Website](https://cupy.dev/)
     """
 
     cc3d = auto()
     scipy = auto()
+    cupy = auto()
 
 
 if __name__ == "__main__":
diff --git a/panoptica/utils/input_check_and_conversion/check_torch_image.py b/panoptica/utils/input_check_and_conversion/check_torch_image.py
index e920097..3806790 100644
--- a/panoptica/utils/input_check_and_conversion/check_torch_image.py
+++ b/panoptica/utils/input_check_and_conversion/check_torch_image.py
@@ -1,17 +1,27 @@
 import numpy as np
 from importlib.util import find_spec
 from pathlib import Path
+from typing import Union, TYPE_CHECKING
 from panoptica.utils.input_check_and_conversion.check_numpy_array import (
     sanity_checker_numpy_array,
 )
 
-# Optional sitk import
+# Optional torch import
 _spec = find_spec("torch")
 if _spec is not None:
     import torch
+else:
+    torch = None
+
+if TYPE_CHECKING:
+    import torch
 
 
-def load_torch_image(image_path: str | Path) -> torch.Tensor:
+def load_torch_image(image_path: Union[str, Path]):
+    if torch is None:
+        raise ImportError(
+            "torch is not available. Please install torch to use this functionality."
+        )
     try:
         image = torch.load(
             image_path,
@@ -25,9 +35,9 @@ def load_torch_image(image_path: str | Path) -> torch.Tensor:
 
 
 def sanity_checker_torch_image(
-    prediction_image: torch.Tensor | str | Path,
-    reference_image: torch.Tensor | str | Path,
-) -> tuple[bool, tuple[np.ndarray, np.ndarray] | str]:
+    prediction_image: Union["torch.Tensor", str, Path],
+    reference_image: Union["torch.Tensor", str, Path],
+) -> tuple[bool, Union[tuple[np.ndarray, np.ndarray], str]]:
     """
     This function performs sanity check on 2 Torch tensors by converting them to numpy arrays and using that check.
 
@@ -38,6 +48,11 @@ def sanity_checker_torch_image(
     Returns:
         tuple[bool, tuple[np.ndarray, np.ndarray] | str]: A tuple where the first element is a boolean indicating if the images pass the sanity check, and the second element is either the numpy arrays of the images or an error message.
     """
+    if torch is None:
+        raise ImportError(
+            "torch is not available. Please install torch to use this functionality."
+        )
+
     # load if necessary
     if isinstance(prediction_image, (str, Path)):
         prediction_image = load_torch_image(prediction_image)
diff --git a/poetry.lock b/poetry.lock
index 758b6b3..9221ce1 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,12 +1,13 @@
-# This file is automatically @generated by Poetry 2.2.0 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand.
 
 [[package]]
 name = "accessible-pygments"
 version = "0.0.5"
 description = "A collection of accessible pygments styles"
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "accessible_pygments-0.0.5-py3-none-any.whl", hash = "sha256:88ae3211e68a1d0b011504b2ffc1691feafce124b845bd072ab6f9f66f34d4b7"},
     {file = "accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872"},
@@ -23,9 +24,10 @@ tests = ["hypothesis", "pytest"]
 name = "alabaster"
 version = "1.0.0"
 description = "A light, configurable Sphinx theme"
-optional = false
+optional = true
 python-versions = ">=3.10"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "alabaster-1.0.0-py3-none-any.whl", hash = "sha256:fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b"},
     {file = "alabaster-1.0.0.tar.gz", hash = "sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e"},
@@ -35,9 +37,10 @@ files = [
 name = "auxiliary"
 version = "0.4.1"
 description = "TODO."
-optional = false
+optional = true
 python-versions = "<4.0,>=3.10"
-groups = ["dev"]
+groups = ["main"]
+markers = "extra == \"test\""
 files = [
     {file = "auxiliary-0.4.1-py3-none-any.whl", hash = "sha256:b35e28f90167a38c1e59d929e08083b2d93f57220cd82497e046a5fe5daef730"},
     {file = "auxiliary-0.4.1.tar.gz", hash = "sha256:425e07dedd48ad00a0532fd10911e4dde02b56b603cb6f6dc4a7488afa482c57"},
@@ -58,9 +61,10 @@ dcm2niix = ["dcm2niix (>=1.0.20250506)"]
 name = "babel"
 version = "2.17.0"
 description = "Internationalization utilities"
-optional = false
+optional = true
 python-versions = ">=3.8"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "babel-2.17.0-py3-none-any.whl", hash = "sha256:4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2"},
     {file = "babel-2.17.0.tar.gz", hash = "sha256:0c54cffb19f690cdcc52a3b50bcbf71e07a808d1c80d549f2459b9d2cf0afb9d"},
@@ -73,9 +77,10 @@ dev = ["backports.zoneinfo ; python_version < \"3.9\"", "freezegun (>=1.0,<2.0)"
 name = "beautifulsoup4"
 version = "4.13.5"
 description = "Screen-scraping library"
-optional = false
+optional = true
 python-versions = ">=3.7.0"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "beautifulsoup4-4.13.5-py3-none-any.whl", hash = "sha256:642085eaa22233aceadff9c69651bc51e8bf3f874fb6d7104ece2beb24b47c4a"},
     {file = "beautifulsoup4-4.13.5.tar.gz", hash = "sha256:5e70131382930e7c3de33450a2f54a63d5e4b19386eab43a5b34d594268f3695"},
@@ -96,9 +101,10 @@ lxml = ["lxml"]
 name = "certifi"
 version = "2025.8.3"
 description = "Python package for providing Mozilla's CA Bundle."
-optional = false
+optional = true
 python-versions = ">=3.7"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "certifi-2025.8.3-py3-none-any.whl", hash = "sha256:f6c12493cfb1b06ba2ff328595af9350c65d6644968e5d3a2ffd78699af217a5"},
     {file = "certifi-2025.8.3.tar.gz", hash = "sha256:e564105f78ded564e3ae7c923924435e1daa7463faeab5bb932bc53ffae63407"},
@@ -108,9 +114,10 @@ files = [
 name = "charset-normalizer"
 version = "3.4.3"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
-optional = false
+optional = true
 python-versions = ">=3.7"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
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@@ -214,12 +221,12 @@ version = "0.4.6"
 description = "Cross-platform colored terminal text."
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
-groups = ["main", "dev", "docs"]
+groups = ["main", "dev"]
 files = [
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 ]
-markers = {main = "platform_system == \"Windows\"", dev = "sys_platform == \"win32\" or platform_system == \"Windows\"", docs = "sys_platform == \"win32\""}
+markers = {main = "(extra == \"test\" or extra == \"docs\") and sys_platform == \"win32\" or platform_system == \"Windows\"", dev = "sys_platform == \"win32\""}
 
 [[package]]
 name = "connected-components-3d"
@@ -369,13 +376,34 @@ files = [
 [package.extras]
 toml = ["tomli ; python_full_version <= \"3.11.0a6\""]
 
+[[package]]
+name = "cupy"
+version = "13.6.0"
+description = "CuPy: NumPy & SciPy for GPU"
+optional = true
+python-versions = ">=3.9"
+groups = ["main"]
+markers = "extra == \"gpu\""
+files = [
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+]
+
+[package.dependencies]
+fastrlock = ">=0.5"
+numpy = ">=1.22,<2.6"
+
+[package.extras]
+all = ["Cython (>=3)", "optuna (>=2.0)", "scipy (>=1.7,<1.17)"]
+test = ["hypothesis (>=6.37.2,<6.55.0)", "mpmath", "packaging", "pytest (>=7.2)"]
+
 [[package]]
 name = "docutils"
 version = "0.21.2"
 description = "Docutils -- Python Documentation Utilities"
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
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@@ -387,12 +415,12 @@ version = "1.3.0"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
-groups = ["dev"]
-markers = "python_version == \"3.10\""
+groups = ["main", "dev"]
 files = [
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 ]
+markers = {main = "extra == \"test\" and python_version == \"3.10\"", dev = "python_version == \"3.10\""}
 
 [package.dependencies]
 typing-extensions = {version = ">=4.6.0", markers = "python_version < \"3.13\""}
@@ -400,6 +428,86 @@ typing-extensions = {version = ">=4.6.0", markers = "python_version < \"3.13\""}
 [package.extras]
 test = ["pytest (>=6)"]
 
+[[package]]
+name = "fastrlock"
+version = "0.8.3"
+description = "Fast, re-entrant optimistic lock implemented in Cython"
+optional = true
+python-versions = "*"
+groups = ["main"]
+markers = "extra == \"gpu\""
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 [[package]]
 name = "filelock"
 version = "3.19.1"
@@ -473,9 +581,10 @@ tqdm = ["tqdm"]
 name = "furo"
 version = "2025.7.19"
 description = "A clean customisable Sphinx documentation theme."
-optional = false
+optional = true
 python-versions = ">=3.8"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "furo-2025.7.19-py3-none-any.whl", hash = "sha256:bdea869822dfd2b494ea84c0973937e35d1575af088b6721a29c7f7878adc9e3"},
     {file = "furo-2025.7.19.tar.gz", hash = "sha256:4164b2cafcf4023a59bb3c594e935e2516f6b9d35e9a5ea83d8f6b43808fe91f"},
@@ -503,9 +612,10 @@ files = [
 name = "idna"
 version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
-optional = false
+optional = true
 python-versions = ">=3.6"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "idna-3.10-py3-none-any.whl", hash = "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"},
     {file = "idna-3.10.tar.gz", hash = "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9"},
@@ -552,9 +662,10 @@ tifffile = ["tifffile"]
 name = "imagesize"
 version = "1.4.1"
 description = "Getting image size from png/jpeg/jpeg2000/gif file"
-optional = false
+optional = true
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "imagesize-1.4.1-py2.py3-none-any.whl", hash = "sha256:0d8d18d08f840c19d0ee7ca1fd82490fdc3729b7ac93f49870406ddde8ef8d8b"},
     {file = "imagesize-1.4.1.tar.gz", hash = "sha256:69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a"},
@@ -564,10 +675,10 @@ files = [
 name = "importlib-resources"
 version = "6.5.2"
 description = "Read resources from Python packages"
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["dev"]
-markers = "python_version < \"3.12\""
+groups = ["main"]
+markers = "python_version < \"3.12\" and extra == \"test\""
 files = [
     {file = "importlib_resources-6.5.2-py3-none-any.whl", hash = "sha256:789cfdc3ed28c78b67a06acb8126751ced69a3d5f79c095a98298cd8a760ccec"},
     {file = "importlib_resources-6.5.2.tar.gz", hash = "sha256:185f87adef5bcc288449d98fb4fba07cea78bc036455dd44c5fc4a2fe78fed2c"},
@@ -587,11 +698,12 @@ version = "2.1.0"
 description = "brain-dead simple config-ini parsing"
 optional = false
 python-versions = ">=3.8"
-groups = ["dev"]
+groups = ["main", "dev"]
 files = [
     {file = "iniconfig-2.1.0-py3-none-any.whl", hash = "sha256:9deba5723312380e77435581c6bf4935c94cbfab9b1ed33ef8d238ea168eb760"},
     {file = "iniconfig-2.1.0.tar.gz", hash = "sha256:3abbd2e30b36733fee78f9c7f7308f2d0050e88f0087fd25c2645f63c773e1c7"},
 ]
+markers = {main = "extra == \"test\""}
 
 [[package]]
 name = "jinja2"
@@ -599,11 +711,12 @@ version = "3.1.6"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
-groups = ["dev", "docs"]
+groups = ["main", "dev"]
 files = [
     {file = "jinja2-3.1.6-py3-none-any.whl", hash = "sha256:85ece4451f492d0c13c5dd7c13a64681a86afae63a5f347908daf103ce6d2f67"},
     {file = "jinja2-3.1.6.tar.gz", hash = "sha256:0137fb05990d35f1275a587e9aee6d56da821fc83491a0fb838183be43f66d6d"},
 ]
+markers = {main = "extra == \"docs\""}
 
 [package.dependencies]
 MarkupSafe = ">=2.0"
@@ -615,9 +728,10 @@ i18n = ["Babel (>=2.7)"]
 name = "joblib"
 version = "1.5.2"
 description = "Lightweight pipelining with Python functions"
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["dev"]
+groups = ["main"]
+markers = "extra == \"test\""
 files = [
     {file = "joblib-1.5.2-py3-none-any.whl", hash = "sha256:4e1f0bdbb987e6d843c70cf43714cb276623def372df3c22fe5266b2670bc241"},
     {file = "joblib-1.5.2.tar.gz", hash = "sha256:3faa5c39054b2f03ca547da9b2f52fde67c06240c31853f306aea97f13647b55"},
@@ -647,9 +761,10 @@ test = ["pytest (>=7.4)", "pytest-cov (>=4.1)"]
 name = "loguru"
 version = "0.7.3"
 description = "Python logging made (stupidly) simple"
-optional = false
+optional = true
 python-versions = "<4.0,>=3.5"
-groups = ["dev"]
+groups = ["main"]
+markers = "extra == \"test\""
 files = [
     {file = "loguru-0.7.3-py3-none-any.whl", hash = "sha256:31a33c10c8e1e10422bfd431aeb5d351c7cf7fa671e3c4df004162264b28220c"},
     {file = "loguru-0.7.3.tar.gz", hash = "sha256:19480589e77d47b8d85b2c827ad95d49bf31b0dcde16593892eb51dd18706eb6"},
@@ -668,7 +783,7 @@ version = "3.0.0"
 description = "Python port of markdown-it. Markdown parsing, done right!"
 optional = false
 python-versions = ">=3.8"
-groups = ["main", "docs"]
+groups = ["main"]
 files = [
     {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"},
     {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"},
@@ -693,7 +808,7 @@ version = "3.0.2"
 description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
 python-versions = ">=3.9"
-groups = ["dev", "docs"]
+groups = ["main", "dev"]
 files = [
     {file = "MarkupSafe-3.0.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:7e94c425039cde14257288fd61dcfb01963e658efbc0ff54f5306b06054700f8"},
     {file = "MarkupSafe-3.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9e2d922824181480953426608b81967de705c3cef4d1af983af849d7bd619158"},
@@ -757,6 +872,7 @@ files = [
     {file = "MarkupSafe-3.0.2-cp39-cp39-win_amd64.whl", hash = "sha256:6e296a513ca3d94054c2c881cc913116e90fd030ad1c656b3869762b754f5f8a"},
     {file = "markupsafe-3.0.2.tar.gz", hash = "sha256:ee55d3edf80167e48ea11a923c7386f4669df67d7994554387f84e7d8b0a2bf0"},
 ]
+markers = {main = "extra == \"docs\""}
 
 [[package]]
 name = "mccabe"
@@ -774,9 +890,10 @@ files = [
 name = "mdit-py-plugins"
 version = "0.5.0"
 description = "Collection of plugins for markdown-it-py"
-optional = false
+optional = true
 python-versions = ">=3.10"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "mdit_py_plugins-0.5.0-py3-none-any.whl", hash = "sha256:07a08422fc1936a5d26d146759e9155ea466e842f5ab2f7d2266dd084c8dab1f"},
     {file = "mdit_py_plugins-0.5.0.tar.gz", hash = "sha256:f4918cb50119f50446560513a8e311d574ff6aaed72606ddae6d35716fe809c6"},
@@ -796,7 +913,7 @@ version = "0.1.2"
 description = "Markdown URL utilities"
 optional = false
 python-versions = ">=3.7"
-groups = ["main", "docs"]
+groups = ["main"]
 files = [
     {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"},
     {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"},
@@ -824,9 +941,10 @@ tests = ["pytest (>=4.6)"]
 name = "myst-parser"
 version = "4.0.1"
 description = "An extended [CommonMark](https://spec.commonmark.org/) compliant parser,"
-optional = false
+optional = true
 python-versions = ">=3.10"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "myst_parser-4.0.1-py3-none-any.whl", hash = "sha256:9134e88959ec3b5780aedf8a99680ea242869d012e8821db3126d427edc9c95d"},
     {file = "myst_parser-4.0.1.tar.gz", hash = "sha256:5cfea715e4f3574138aecbf7d54132296bfd72bb614d31168f48c477a830a7c4"},
@@ -894,9 +1012,10 @@ test-extras = ["pytest-mpl", "pytest-randomly"]
 name = "nibabel"
 version = "5.3.2"
 description = "Access a multitude of neuroimaging data formats"
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["dev"]
+groups = ["main"]
+markers = "extra == \"test\""
 files = [
     {file = "nibabel-5.3.2-py3-none-any.whl", hash = "sha256:52970a5a8a53b1b55249cba4d9bcfaa8cc57e3e5af35a29d7352237e8680a6f8"},
     {file = "nibabel-5.3.2.tar.gz", hash = "sha256:0bdca6503b1c784b446c745a4542367de7756cfba0d72143b91f9ffb78be569b"},
@@ -928,7 +1047,7 @@ version = "2.2.6"
 description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.10"
-groups = ["main", "dev"]
+groups = ["main"]
 files = [
     {file = "numpy-2.2.6-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b412caa66f72040e6d268491a59f2c43bf03eb6c96dd8f0307829feb7fa2b6fb"},
     {file = "numpy-2.2.6-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8e41fd67c52b86603a91c1a505ebaef50b3314de0213461c7a6e99c9a3beff90"},
@@ -1423,7 +1542,7 @@ version = "25.0"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.8"
-groups = ["main", "dev", "docs"]
+groups = ["main", "dev"]
 files = [
     {file = "packaging-25.0-py3-none-any.whl", hash = "sha256:29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484"},
     {file = "packaging-25.0.tar.gz", hash = "sha256:d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f"},
@@ -1520,9 +1639,10 @@ xml = ["lxml (>=4.9.2)"]
 name = "path"
 version = "17.1.1"
 description = "A module wrapper for os.path"
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["dev"]
+groups = ["main"]
+markers = "extra == \"test\""
 files = [
     {file = "path-17.1.1-py3-none-any.whl", hash = "sha256:ec7e136df29172e5030dd07e037d55f676bdb29d15bfa09b80da29d07d3b9303"},
     {file = "path-17.1.1.tar.gz", hash = "sha256:2dfcbfec8b4d960f3469c52acf133113c2a8bf12ac7b98d629fa91af87248d42"},
@@ -1542,7 +1662,7 @@ version = "11.3.0"
 description = "Python Imaging Library (Fork)"
 optional = false
 python-versions = ">=3.9"
-groups = ["main", "dev"]
+groups = ["main"]
 files = [
     {file = "pillow-11.3.0-cp310-cp310-macosx_10_10_x86_64.whl", hash = "sha256:1b9c17fd4ace828b3003dfd1e30bff24863e0eb59b535e8f80194d9cc7ecf860"},
     {file = "pillow-11.3.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:65dc69160114cdd0ca0f35cb434633c75e8e7fad4cf855177a05bf38678f73ad"},
@@ -1683,11 +1803,12 @@ version = "1.6.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.9"
-groups = ["dev"]
+groups = ["main", "dev"]
 files = [
     {file = "pluggy-1.6.0-py3-none-any.whl", hash = "sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746"},
     {file = "pluggy-1.6.0.tar.gz", hash = "sha256:7dcc130b76258d33b90f61b658791dede3486c3e6bfb003ee5c9bfb396dd22f3"},
 ]
+markers = {main = "extra == \"test\""}
 
 [package.extras]
 dev = ["pre-commit", "tox"]
@@ -1723,7 +1844,7 @@ version = "2.19.2"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.8"
-groups = ["main", "dev", "docs"]
+groups = ["main", "dev"]
 files = [
     {file = "pygments-2.19.2-py3-none-any.whl", hash = "sha256:86540386c03d588bb81d44bc3928634ff26449851e99741617ecb9037ee5ec0b"},
     {file = "pygments-2.19.2.tar.gz", hash = "sha256:636cb2477cec7f8952536970bc533bc43743542f70392ae026374600add5b887"},
@@ -1736,9 +1857,10 @@ windows-terminal = ["colorama (>=0.4.6)"]
 name = "pynrrd"
 version = "1.1.3"
 description = "Pure python module for reading and writing NRRD files."
-optional = false
+optional = true
 python-versions = ">=3.7"
-groups = ["dev"]
+groups = ["main"]
+markers = "extra == \"test\""
 files = [
     {file = "pynrrd-1.1.3-py3-none-any.whl", hash = "sha256:21f7e370045e7ef8a86841965b2ff3a18937efbb4e2078e346168463f8f34b7e"},
     {file = "pynrrd-1.1.3.tar.gz", hash = "sha256:a331263bc9f05c3168182e61d6098e256a34e0fadbb7427a1d086d8942fbcbe0"},
@@ -1757,11 +1879,12 @@ version = "8.4.2"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.9"
-groups = ["dev"]
+groups = ["main", "dev"]
 files = [
     {file = "pytest-8.4.2-py3-none-any.whl", hash = "sha256:872f880de3fc3a5bdc88a11b39c9710c3497a547cfa9320bc3c5e62fbf272e79"},
     {file = "pytest-8.4.2.tar.gz", hash = "sha256:86c0d0b93306b961d58d62a4db4879f27fe25513d4b969df351abdddb3c30e01"},
 ]
+markers = {main = "extra == \"test\""}
 
 [package.dependencies]
 colorama = {version = ">=0.4", markers = "sys_platform == \"win32\""}
@@ -1824,9 +1947,10 @@ files = [
 name = "pyyaml"
 version = "6.0.2"
 description = "YAML parser and emitter for Python"
-optional = false
+optional = true
 python-versions = ">=3.8"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "PyYAML-6.0.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:0a9a2848a5b7feac301353437eb7d5957887edbf81d56e903999a75a3d743086"},
     {file = "PyYAML-6.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:29717114e51c84ddfba879543fb232a6ed60086602313ca38cce623c1d62cfbf"},
@@ -1887,9 +2011,10 @@ files = [
 name = "requests"
 version = "2.32.5"
 description = "Python HTTP for Humans."
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "requests-2.32.5-py3-none-any.whl", hash = "sha256:2462f94637a34fd532264295e186976db0f5d453d1cdd31473c85a6a161affb6"},
     {file = "requests-2.32.5.tar.gz", hash = "sha256:dbba0bac56e100853db0ea71b82b4dfd5fe2bf6d3754a8893c3af500cec7d7cf"},
@@ -1929,10 +2054,10 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 name = "roman-numerals-py"
 version = "3.1.0"
 description = "Manipulate well-formed Roman numerals"
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["docs"]
-markers = "python_version >= \"3.11\""
+groups = ["main"]
+markers = "python_version >= \"3.11\" and extra == \"docs\""
 files = [
     {file = "roman_numerals_py-3.1.0-py3-none-any.whl", hash = "sha256:9da2ad2fb670bcf24e81070ceb3be72f6c11c440d73bd579fbeca1e9f330954c"},
     {file = "roman_numerals_py-3.1.0.tar.gz", hash = "sha256:be4bf804f083a4ce001b5eb7e3c0862479d10f94c936f6c4e5f250aa5ff5bd2d"},
@@ -2251,9 +2376,10 @@ files = [
 name = "simpleitk"
 version = "2.5.2"
 description = "SimpleITK is a simplified interface to the Insight Toolkit (ITK) for image registration and segmentation"
-optional = false
+optional = true
 python-versions = "*"
-groups = ["dev"]
+groups = ["main"]
+markers = "extra == \"test\""
 files = [
     {file = "simpleitk-2.5.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:ddfae02f6fc67829fcf13cffb22e8ff9d5cc79d6453d546c9937c1abafa7d257"},
     {file = "simpleitk-2.5.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:76ec652d30762adfedb167fc8fe3918099f0b87397c7656a0bab1ba21cb2dfcd"},
@@ -2288,9 +2414,10 @@ files = [
 name = "snowballstemmer"
 version = "3.0.1"
 description = "This package provides 32 stemmers for 30 languages generated from Snowball algorithms."
-optional = false
+optional = true
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "snowballstemmer-3.0.1-py3-none-any.whl", hash = "sha256:6cd7b3897da8d6c9ffb968a6781fa6532dce9c3618a4b127d920dab764a19064"},
     {file = "snowballstemmer-3.0.1.tar.gz", hash = "sha256:6d5eeeec8e9f84d4d56b847692bacf79bc2c8e90c7f80ca4444ff8b6f2e52895"},
@@ -2300,9 +2427,10 @@ files = [
 name = "soupsieve"
 version = "2.8"
 description = "A modern CSS selector implementation for Beautiful Soup."
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "soupsieve-2.8-py3-none-any.whl", hash = "sha256:0cc76456a30e20f5d7f2e14a98a4ae2ee4e5abdc7c5ea0aafe795f344bc7984c"},
     {file = "soupsieve-2.8.tar.gz", hash = "sha256:e2dd4a40a628cb5f28f6d4b0db8800b8f581b65bb380b97de22ba5ca8d72572f"},
@@ -2312,10 +2440,10 @@ files = [
 name = "sphinx"
 version = "8.1.3"
 description = "Python documentation generator"
-optional = false
+optional = true
 python-versions = ">=3.10"
-groups = ["docs"]
-markers = "python_version == \"3.10\""
+groups = ["main"]
+markers = "python_version == \"3.10\" and extra == \"docs\""
 files = [
     {file = "sphinx-8.1.3-py3-none-any.whl", hash = "sha256:09719015511837b76bf6e03e42eb7595ac8c2e41eeb9c29c5b755c6b677992a2"},
     {file = "sphinx-8.1.3.tar.gz", hash = "sha256:43c1911eecb0d3e161ad78611bc905d1ad0e523e4ddc202a58a821773dc4c927"},
@@ -2349,10 +2477,10 @@ test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "setuptools
 name = "sphinx"
 version = "8.2.3"
 description = "Python documentation generator"
-optional = false
+optional = true
 python-versions = ">=3.11"
-groups = ["docs"]
-markers = "python_version >= \"3.11\""
+groups = ["main"]
+markers = "python_version >= \"3.11\" and extra == \"docs\""
 files = [
     {file = "sphinx-8.2.3-py3-none-any.whl", hash = "sha256:4405915165f13521d875a8c29c8970800a0141c14cc5416a38feca4ea5d9b9c3"},
     {file = "sphinx-8.2.3.tar.gz", hash = "sha256:398ad29dee7f63a75888314e9424d40f52ce5a6a87ae88e7071e80af296ec348"},
@@ -2386,9 +2514,10 @@ test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "pytest-xdis
 name = "sphinx-basic-ng"
 version = "1.0.0b2"
 description = "A modern skeleton for Sphinx themes."
-optional = false
+optional = true
 python-versions = ">=3.7"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "sphinx_basic_ng-1.0.0b2-py3-none-any.whl", hash = "sha256:eb09aedbabfb650607e9b4b68c9d240b90b1e1be221d6ad71d61c52e29f7932b"},
     {file = "sphinx_basic_ng-1.0.0b2.tar.gz", hash = "sha256:9ec55a47c90c8c002b5960c57492ec3021f5193cb26cebc2dc4ea226848651c9"},
@@ -2404,9 +2533,10 @@ docs = ["furo", "ipython", "myst-parser", "sphinx-copybutton", "sphinx-inline-ta
 name = "sphinx-copybutton"
 version = "0.5.2"
 description = "Add a copy button to each of your code cells."
-optional = false
+optional = true
 python-versions = ">=3.7"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "sphinx-copybutton-0.5.2.tar.gz", hash = "sha256:4cf17c82fb9646d1bc9ca92ac280813a3b605d8c421225fd9913154103ee1fbd"},
     {file = "sphinx_copybutton-0.5.2-py3-none-any.whl", hash = "sha256:fb543fd386d917746c9a2c50360c7905b605726b9355cd26e9974857afeae06e"},
@@ -2423,9 +2553,10 @@ rtd = ["ipython", "myst-nb", "sphinx", "sphinx-book-theme", "sphinx-examples"]
 name = "sphinxcontrib-applehelp"
 version = "2.0.0"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "sphinxcontrib_applehelp-2.0.0-py3-none-any.whl", hash = "sha256:4cd3f0ec4ac5dd9c17ec65e9ab272c9b867ea77425228e68ecf08d6b28ddbdb5"},
     {file = "sphinxcontrib_applehelp-2.0.0.tar.gz", hash = "sha256:2f29ef331735ce958efa4734873f084941970894c6090408b079c61b2e1c06d1"},
@@ -2440,9 +2571,10 @@ test = ["pytest"]
 name = "sphinxcontrib-devhelp"
 version = "2.0.0"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "sphinxcontrib_devhelp-2.0.0-py3-none-any.whl", hash = "sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2"},
     {file = "sphinxcontrib_devhelp-2.0.0.tar.gz", hash = "sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad"},
@@ -2457,9 +2589,10 @@ test = ["pytest"]
 name = "sphinxcontrib-htmlhelp"
 version = "2.1.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl", hash = "sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8"},
     {file = "sphinxcontrib_htmlhelp-2.1.0.tar.gz", hash = "sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9"},
@@ -2474,9 +2607,10 @@ test = ["html5lib", "pytest"]
 name = "sphinxcontrib-jsmath"
 version = "1.0.1"
 description = "A sphinx extension which renders display math in HTML via JavaScript"
-optional = false
+optional = true
 python-versions = ">=3.5"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "sphinxcontrib-jsmath-1.0.1.tar.gz", hash = "sha256:a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8"},
     {file = "sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl", hash = "sha256:2ec2eaebfb78f3f2078e73666b1415417a116cc848b72e5172e596c871103178"},
@@ -2489,9 +2623,10 @@ test = ["flake8", "mypy", "pytest"]
 name = "sphinxcontrib-qthelp"
 version = "2.0.0"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "sphinxcontrib_qthelp-2.0.0-py3-none-any.whl", hash = "sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb"},
     {file = "sphinxcontrib_qthelp-2.0.0.tar.gz", hash = "sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab"},
@@ -2506,9 +2641,10 @@ test = ["defusedxml (>=0.7.1)", "pytest"]
 name = "sphinxcontrib-serializinghtml"
 version = "2.0.0"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl", hash = "sha256:6e2cb0eef194e10c27ec0023bfeb25badbbb5868244cf5bc5bdc04e4464bf331"},
     {file = "sphinxcontrib_serializinghtml-2.0.0.tar.gz", hash = "sha256:e9d912827f872c029017a53f0ef2180b327c3f7fd23c87229f7a8e8b70031d4d"},
@@ -2559,7 +2695,7 @@ version = "2025.5.10"
 description = "Read and write TIFF files"
 optional = false
 python-versions = ">=3.10"
-groups = ["main", "dev"]
+groups = ["main"]
 markers = "python_version == \"3.10\""
 files = [
     {file = "tifffile-2025.5.10-py3-none-any.whl", hash = "sha256:e37147123c0542d67bc37ba5cdd67e12ea6fbe6e86c52bee037a9eb6a064e5ad"},
@@ -2583,7 +2719,7 @@ version = "2025.9.9"
 description = "Read and write TIFF files"
 optional = false
 python-versions = ">=3.11"
-groups = ["main", "dev"]
+groups = ["main"]
 markers = "python_version >= \"3.11\""
 files = [
     {file = "tifffile-2025.9.9-py3-none-any.whl", hash = "sha256:239247551fa10b5679036ee030cdbeb7762bc1b3f11b1ddaaf50759ef8b4eb26"},
@@ -2607,8 +2743,7 @@ version = "2.2.1"
 description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.8"
-groups = ["dev", "docs"]
-markers = "python_version == \"3.10\""
+groups = ["main", "dev"]
 files = [
     {file = "tomli-2.2.1-cp311-cp311-macosx_10_9_x86_64.whl", hash = "sha256:678e4fa69e4575eb77d103de3df8a895e1591b48e740211bd1067378c69e8249"},
     {file = "tomli-2.2.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:023aa114dd824ade0100497eb2318602af309e5a55595f76b626d6d9f3b7b0a6"},
@@ -2643,6 +2778,7 @@ files = [
     {file = "tomli-2.2.1-py3-none-any.whl", hash = "sha256:cb55c73c5f4408779d0cf3eef9f762b9c9f147a77de7b258bef0a5628adc85cc"},
     {file = "tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff"},
 ]
+markers = {main = "(extra == \"test\" or extra == \"docs\") and python_version == \"3.10\"", dev = "python_version == \"3.10\""}
 
 [[package]]
 name = "torch"
@@ -2774,9 +2910,10 @@ pyyaml = ["pyyaml"]
 name = "tqdm"
 version = "4.67.1"
 description = "Fast, Extensible Progress Meter"
-optional = false
+optional = true
 python-versions = ">=3.7"
-groups = ["dev"]
+groups = ["main"]
+markers = "extra == \"test\""
 files = [
     {file = "tqdm-4.67.1-py3-none-any.whl", hash = "sha256:26445eca388f82e72884e0d580d5464cd801a3ea01e63e5601bdff9ba6a48de2"},
     {file = "tqdm-4.67.1.tar.gz", hash = "sha256:f8aef9c52c08c13a65f30ea34f4e5aac3fd1a34959879d7e59e63027286627f2"},
@@ -2866,7 +3003,7 @@ version = "4.15.0"
 description = "Backported and Experimental Type Hints for Python 3.9+"
 optional = false
 python-versions = ">=3.9"
-groups = ["main", "dev", "docs"]
+groups = ["main", "dev"]
 files = [
     {file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"},
     {file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"},
@@ -2888,9 +3025,10 @@ files = [
 name = "urllib3"
 version = "2.5.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
-optional = false
+optional = true
 python-versions = ">=3.9"
-groups = ["docs"]
+groups = ["main"]
+markers = "extra == \"docs\""
 files = [
     {file = "urllib3-2.5.0-py3-none-any.whl", hash = "sha256:e6b01673c0fa6a13e374b50871808eb3bf7046c4b125b216f6bf1cc604cff0dc"},
     {file = "urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760"},
@@ -2906,10 +3044,10 @@ zstd = ["zstandard (>=0.18.0)"]
 name = "win32-setctime"
 version = "1.2.0"
 description = "A small Python utility to set file creation time on Windows"
-optional = false
+optional = true
 python-versions = ">=3.5"
-groups = ["dev"]
-markers = "sys_platform == \"win32\""
+groups = ["main"]
+markers = "extra == \"test\" and sys_platform == \"win32\""
 files = [
     {file = "win32_setctime-1.2.0-py3-none-any.whl", hash = "sha256:95d644c4e708aba81dc3704a116d8cbc974d70b3bdb8be1d150e36be6e9d1390"},
     {file = "win32_setctime-1.2.0.tar.gz", hash = "sha256:ae1fdf948f5640aae05c511ade119313fb6a30d7eabe25fef9764dca5873c4c0"},
@@ -2918,7 +3056,12 @@ files = [
 [package.extras]
 dev = ["black (>=19.3b0) ; python_version >= \"3.6\"", "pytest (>=4.6.2)"]
 
+[extras]
+docs = ["Sphinx", "furo", "myst-parser", "sphinx-copybutton"]
+gpu = ["cupy"]
+test = ["SimpleITK", "auxiliary", "joblib", "nibabel", "pynrrd", "pytest", "tqdm"]
+
 [metadata]
 lock-version = "2.1"
-python-versions = "^3.10"
-content-hash = "f57e595a27ca3a87a1c8f5338b21e0a06031c4426fc730af9ec96d6e653e8333"
+python-versions = ">=3.10,<4.0"
+content-hash = "8726eb553a9a36550a67ac718bddee671f650bb25d685fa69295edbf7c45ea07"
diff --git a/pyproject.toml b/pyproject.toml
index e79212e..3a28b04 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,56 +6,69 @@ build-backend = "poetry_dynamic_versioning.backend"
 enable = true
 
 [tool.poetry]
+exclude = ["examples", "benchmark"]
+
+[project]
 name = "panoptica"
 version = "0.0.0"
 description = "Panoptic Quality (PQ) computation for binary masks."
 authors = [
-    "Hendrik Möller <hendrik.moeller@tum.de>",
-    "Florian Kofler <florian.kofler@tum.de>",
+    { name = "Hendrik Möller", email = "hendrik.moeller@tum.de" },
+    { name = "Florian Kofler", email = "florian.kofler@tum.de" },
+]
+readme = "README.md"
+requires-python = ">=3.10,<4.0"
+license = { file = "LICENSE" }
+keywords = ["panoptic", "quality", "segmentation", "medical imaging"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
 ]
+dependencies = [
+    "numpy>=1.22,<2.3",
+    "connected-components-3d>=3.12.3,<4.0.0",
+    "scipy>=1.7.0,<2.0.0",
+    "rich>=13.6.0,<14.0.0",
+    "scikit-image>=0.22.0,<1.0.0",
+    "ruamel.yaml>=0.18.6,<1.0.0",
+    "plotly>=5.16.1,<6.0.0",
+    "pandas>=2.1.0,<3.0.0",
+    "typer>=0.15.0,<1.0.0",
+]
+
+[project.urls]
 repository = "https://github.com/BrainLesion/panoptica"
 homepage = "https://github.com/BrainLesion/panoptica"
 documentation = "https://panoptica.readthedocs.io/"
-readme = "README.md"
-
-
-# Add the exclude field directly under [tool.poetry]
-exclude = ["examples", "benchmark"]
-
-[tool.poetry.dependencies]
-python = "^3.10"
-numpy = ">=1.22,<2.3"
-connected-components-3d = "^3.12.3"
-scipy = "^1.7.0"
-rich = "^13.6.0"
-scikit-image = ">=0.22.0, <1.0.0"
-"ruamel.yaml" = ">=0.18.6, <1.0.0"
-plotly = "^5.16.1"
-pandas = "^2.1.0"
-typer = ">=0.15.0, <1.0.0"
 
 [tool.poetry.group.dev.dependencies]
-pytest = ">=8.1.1"
 coverage = ">=7.0.1"
 pytest-mock = "^3.6.0"
-joblib = "^1.3.2"
 future = ">=0.18.3, <1.0.0"
 flake8 = ">=4.0.1"
-auxiliary = ">=0.1.0"
-tqdm = ">=4.62.3"
-SimpleITK = "^2.2.2"
 torch = "^2.1.0"
-nibabel = "^5.1.0"
-pynrrd = "^1.1.3"
 
-[tool.poetry.group.docs]
-optional = true
 
-[tool.poetry.group.docs.dependencies]
-Sphinx = ">=7.0.0"
-sphinx-copybutton = ">=0.5.2, <1.0.0"
-furo = ">=2024.8.6"
-myst-parser = ">=2.0.0"
+[project.optional-dependencies]
+test = [
+    "pytest>=8.1.1",
+    "SimpleITK>=2.2.2,<3.0.0",
+    "nibabel>=5.1.0,<6.0.0",
+    "pynrrd>=1.1.3,<2.0.0",
+    "joblib>=1.3.2,<2.0.0",
+    "tqdm>=4.62.3",
+    "auxiliary>=0.1.0",
+]
+docs = [
+    "Sphinx>=7.0.0",
+    "sphinx-copybutton>=0.5.2,<1.0.0",
+    "furo>=2024.8.6",
+    "myst-parser>=2.0.0",
+]
+gpu = [
+    "cupy>=12.0.0",
+]
 
 [tool.poetry.scripts]
 panopticacli = "panoptica.cli:app"
diff --git a/unit_tests/test_config.py b/unit_tests/test_config.py
index b6e4ccd..a93a3c9 100644
--- a/unit_tests/test_config.py
+++ b/unit_tests/test_config.py
@@ -123,7 +123,7 @@ def test_SegmentationClassGroups_config_by_name(self):
             self.assertEqual(len(t[k].value_labels), len(v.value_labels))
 
     def test_InstanceApproximator_config(self):
-        for backend in [None, CCABackend.cc3d, CCABackend.scipy]:
+        for backend in [None, CCABackend.cc3d, CCABackend.scipy, CCABackend.cupy]:
             t = ConnectedComponentsInstanceApproximator(cca_backend=backend)
             print(t)
             print()
diff --git a/unit_tests/test_cupy_connected_components.py b/unit_tests/test_cupy_connected_components.py
new file mode 100644
index 0000000..5615c50
--- /dev/null
+++ b/unit_tests/test_cupy_connected_components.py
@@ -0,0 +1,264 @@
+# Unit tests for CuPy connected components functionality
+import os
+import unittest
+import numpy as np
+from unittest.mock import patch, MagicMock
+
+from panoptica.utils.constants import CCABackend
+from panoptica._functionals import _connected_components
+from panoptica import ConnectedComponentsInstanceApproximator
+from panoptica.utils.processing_pair import SemanticPair
+
+
+class Test_CuPy_Connected_Components(unittest.TestCase):
+    def setUp(self) -> None:
+        os.environ["PANOPTICA_CITATION_REMINDER"] = "False"
+        return super().setUp()
+
+    def create_test_binary_array(self):
+        """Create a simple test binary array with known connected components."""
+        # Create a 3D array with 3 separate connected components
+        arr = np.zeros((10, 10, 10), dtype=np.bool_)
+
+        # Component 1: small cube in corner
+        arr[1:3, 1:3, 1:3] = True
+
+        # Component 2: larger block in middle
+        arr[4:7, 4:7, 4:7] = True
+
+        # Component 3: single isolated voxel
+        arr[8, 8, 8] = True
+
+        return arr
+
+    def test_cupy_backend_enum_exists(self):
+        """Test that CuPy backend is properly defined in the enum."""
+        self.assertTrue(hasattr(CCABackend, "cupy"))
+        self.assertEqual(CCABackend.cupy.name, "cupy")
+
+    def test_cupy_not_available_error(self):
+        """Test that proper error is raised when CuPy is not available."""
+        test_array = self.create_test_binary_array()
+
+        # Mock the import to fail
+        with patch(
+            "builtins.__import__", side_effect=ImportError("No module named 'cupy'")
+        ):
+            with self.assertRaises(ImportError) as context:
+                _connected_components(test_array, CCABackend.cupy)
+
+            self.assertIn("CuPy is not installed", str(context.exception))
+            self.assertIn("pip install cupy-cuda", str(context.exception))
+
+    def test_cupy_connected_components_function(self):
+        """Test the _connected_components function with CuPy backend."""
+        test_array = self.create_test_binary_array()
+
+        try:
+            # Try to call the function - it should either work or raise ImportError
+            result_array, result_n_components = _connected_components(
+                test_array, CCABackend.cupy
+            )
+
+            # If CuPy is available, verify basic properties
+            self.assertEqual(result_array.shape, test_array.shape)
+            self.assertGreaterEqual(result_n_components, 0)
+
+        except (ImportError, Exception) as e:
+            # CuPy not available or CUDA issues, skip this test
+            if "CUDA" in str(e) or "cupy" in str(e).lower():
+                self.skipTest(
+                    f"CuPy/CUDA not available for connected components test: {e}"
+                )
+            else:
+                raise
+
+    def test_cupy_backend_comparison_with_scipy(self):
+        """Test that CuPy and SciPy backends produce similar results (when CuPy is available)."""
+        test_array = self.create_test_binary_array()
+
+        try:
+            # Try to get results from both backends
+            scipy_result, scipy_n = _connected_components(test_array, CCABackend.scipy)
+            cupy_result, cupy_n = _connected_components(test_array, CCABackend.cupy)
+
+            # Both should find the same number of components
+            self.assertEqual(scipy_n, cupy_n)
+
+            # The label values might be different, but the structure should be the same
+            # Check that both arrays have the same shape and dtype
+            self.assertEqual(scipy_result.shape, cupy_result.shape)
+
+            # Check that both find the same connected regions (regardless of label values)
+            scipy_unique = len(np.unique(scipy_result)) - 1  # subtract 1 for background
+            cupy_unique = len(np.unique(cupy_result)) - 1  # subtract 1 for background
+            self.assertEqual(scipy_unique, cupy_unique)
+
+        except (ImportError, Exception) as e:
+            # CuPy not available or CUDA issues, skip this test
+            if "CUDA" in str(e) or "cupy" in str(e).lower():
+                self.skipTest(f"CuPy/CUDA not available for comparison test: {e}")
+            else:
+                raise
+
+    def test_instance_approximator_with_cupy_backend(self):
+        """Test ConnectedComponentsInstanceApproximator with CuPy backend."""
+        try:
+            # Create test semantic arrays
+            pred_arr = np.zeros((10, 10, 10), dtype=np.uint8)
+            ref_arr = np.zeros((10, 10, 10), dtype=np.uint8)
+
+            # Add some semantic labels
+            pred_arr[2:5, 2:5, 2:5] = 1  # One region
+            pred_arr[6:8, 6:8, 6:8] = 1  # Another region (same semantic class)
+
+            ref_arr[1:4, 1:4, 1:4] = 1  # Overlapping region
+            ref_arr[7:9, 7:9, 7:9] = 1  # Another overlapping region
+
+            # Create semantic pair
+            semantic_pair = SemanticPair(pred_arr, ref_arr)
+
+            # Create approximator with CuPy backend
+            approximator = ConnectedComponentsInstanceApproximator(
+                cca_backend=CCABackend.cupy
+            )
+
+            # Test approximation
+            result = approximator.approximate_instances(semantic_pair)
+
+            # Verify that we get an UnmatchedInstancePair
+            from panoptica.utils.processing_pair import UnmatchedInstancePair
+
+            self.assertIsInstance(result, UnmatchedInstancePair)
+
+            # Verify that instances were found
+            self.assertGreater(result.n_prediction_instance, 0)
+            self.assertGreater(result.n_reference_instance, 0)
+
+        except (ImportError, Exception) as e:
+            # CuPy not available or CUDA issues, skip this test
+            if "CUDA" in str(e) or "cupy" in str(e).lower():
+                self.skipTest(
+                    f"CuPy/CUDA not available for instance approximator test: {e}"
+                )
+            else:
+                raise
+
+    def test_cupy_backend_config_serialization(self):
+        """Test that CuPy backend can be serialized/deserialized in config."""
+        from pathlib import Path
+
+        test_file = Path(__file__).parent.joinpath("test_cupy.yaml")
+
+        try:
+            # Test CuPy backend serialization
+            backend = CCABackend.cupy
+            backend.save_to_config(test_file)
+
+            loaded_backend = CCABackend.load_from_config(test_file)
+            self.assertEqual(backend, loaded_backend)
+
+            # Test with ConnectedComponentsInstanceApproximator
+            approximator = ConnectedComponentsInstanceApproximator(
+                cca_backend=CCABackend.cupy
+            )
+            approximator.save_to_config(test_file)
+
+            loaded_approximator = (
+                ConnectedComponentsInstanceApproximator.load_from_config(test_file)
+            )
+            self.assertEqual(loaded_approximator.cca_backend, CCABackend.cupy)
+
+        finally:
+            # Clean up
+            if test_file.exists():
+                os.remove(test_file)
+
+    def test_various_array_shapes_with_cupy(self):
+        """Test CuPy backend with different array shapes and dimensions."""
+        test_shapes = [
+            (50, 50),  # 2D
+            (20, 20, 20),  # 3D
+            (10, 10, 10, 10),  # 4D
+        ]
+
+        for shape in test_shapes:
+            with self.subTest(shape=shape):
+                try:
+                    # Create test array
+                    arr = np.zeros(shape, dtype=np.bool_)
+                    # Add a small component
+                    slices = tuple(slice(1, 3) for _ in range(len(shape)))
+                    arr[slices] = True
+
+                    # Test with CuPy
+                    result_arr, n_components = _connected_components(
+                        arr, CCABackend.cupy
+                    )
+
+                    # Should find at least one component
+                    self.assertGreaterEqual(n_components, 1)
+                    self.assertEqual(result_arr.shape, arr.shape)
+
+                except (ImportError, Exception) as e:
+                    # CuPy not available or CUDA issues
+                    if "CUDA" in str(e) or "cupy" in str(e).lower():
+                        self.skipTest(
+                            f"CuPy/CUDA not available for shape {shape} test: {e}"
+                        )
+                    else:
+                        raise
+
+    def test_empty_array_with_cupy(self):
+        """Test CuPy backend with empty arrays."""
+        try:
+            empty_arr = np.zeros((10, 10, 10), dtype=np.bool_)
+
+            result_arr, n_components = _connected_components(empty_arr, CCABackend.cupy)
+
+            # Should find no components
+            self.assertEqual(n_components, 0)
+            self.assertEqual(result_arr.shape, empty_arr.shape)
+            # All values should be 0 (background)
+            self.assertEqual(np.max(result_arr), 0)
+
+        except (ImportError, Exception) as e:
+            if "CUDA" in str(e) or "cupy" in str(e).lower():
+                self.skipTest(f"CuPy/CUDA not available for empty array test: {e}")
+            else:
+                raise
+
+    def test_cupy_backend_with_large_array(self):
+        """Test CuPy backend with larger arrays to verify GPU memory handling."""
+        try:
+            # Create a larger test array
+            large_arr = np.zeros((100, 100, 50), dtype=np.bool_)
+
+            # Add several components
+            large_arr[10:20, 10:20, 10:20] = True  # Component 1
+            large_arr[30:40, 30:40, 30:40] = True  # Component 2
+            large_arr[60:70, 60:70, 10:20] = True  # Component 3
+            large_arr[80:90, 10:20, 30:40] = True  # Component 4
+
+            result_arr, n_components = _connected_components(large_arr, CCABackend.cupy)
+
+            # Should find 4 components
+            self.assertEqual(n_components, 4)
+            self.assertEqual(result_arr.shape, large_arr.shape)
+
+            # Verify that we have the right number of unique labels (including background)
+            unique_labels = np.unique(result_arr)
+            self.assertEqual(len(unique_labels), 5)  # 4 components + background (0)
+
+        except ImportError:
+            self.skipTest("CuPy not available for large array test")
+        except Exception as e:
+            # If GPU memory issues or other CUDA errors, skip
+            if "CUDA" in str(e) or "memory" in str(e).lower():
+                self.skipTest(f"GPU/CUDA issues: {e}")
+            else:
+                raise
+
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/unit_tests/test_input_sanity_checker.py b/unit_tests/test_input_sanity_checker.py
index 8e68ae8..bda4039 100644
--- a/unit_tests/test_input_sanity_checker.py
+++ b/unit_tests/test_input_sanity_checker.py
@@ -9,8 +9,18 @@
 import SimpleITK as sitk
 from unittest import mock
 import nibabel as nib
-import torch
 import nrrd
+from importlib.util import find_spec
+
+# Optional torch import
+_spec = find_spec("torch")
+if _spec is not None:
+    import torch
+
+    HAS_TORCH = True
+else:
+    torch = None
+    HAS_TORCH = False
 
 from panoptica.utils.input_check_and_conversion.sanity_checker import (
     sanity_check_and_convert_to_array,
@@ -324,6 +334,7 @@ def test_sanity_checker_without_package(self, *args):
         os.remove(test_nii_file)
 
 
+@unittest.skipUnless(HAS_TORCH, "torch not available")
 class Test_Input_Sanity_Checker_Torch(unittest.TestCase):
     def setUp(self) -> None:
         os.environ["PANOPTICA_CITATION_REMINDER"] = "False"
diff --git a/unit_tests/test_region_comprehensive.py b/unit_tests/test_region_comprehensive.py
new file mode 100644
index 0000000..742d5cc
--- /dev/null
+++ b/unit_tests/test_region_comprehensive.py
@@ -0,0 +1,159 @@
+#!/usr/bin/env python3
+"""
+Comprehensive test suite for RegionBasedMatching implementation
+"""
+
+import numpy as np
+from panoptica.panoptica_evaluator import panoptic_evaluate
+from panoptica.instance_matcher import RegionBasedMatching
+from panoptica.instance_approximator import ConnectedComponentsInstanceApproximator
+from panoptica.metrics import Metric
+from panoptica.utils.constants import CCABackend
+from panoptica.utils.processing_pair import SemanticPair
+
+
+def test_scenario_1_basic():
+    """Test basic case with non-overlapping regions"""
+    print("Test 1: Basic non-overlapping regions")
+
+    gt = np.zeros((30, 30, 10), dtype=np.int32)
+    pred = np.zeros((30, 30, 10), dtype=np.int32)
+
+    # GT regions
+    gt[5:15, 5:15, 2:8] = 1
+    gt[20:25, 20:25, 2:8] = 2
+
+    # Pred regions - slightly offset
+    pred[6:16, 6:16, 3:9] = 1
+    pred[19:24, 19:24, 3:9] = 2
+
+    return gt, pred
+
+
+def test_scenario_2_overlapping():
+    """Test case with overlapping predictions"""
+    print("Test 2: Overlapping predictions")
+
+    gt = np.zeros((30, 30, 10), dtype=np.int32)
+    pred = np.zeros((30, 30, 10), dtype=np.int32)
+
+    # GT regions
+    gt[5:15, 5:15, 2:8] = 1
+    gt[20:25, 20:25, 2:8] = 2
+
+    # Overlapping predictions
+    pred[8:18, 8:18, 3:9] = 1  # Overlaps with both GT regions
+    pred[21:26, 21:26, 3:9] = 2
+
+    return gt, pred
+
+
+def test_scenario_3_empty_prediction():
+    """Test case with no predictions"""
+    print("Test 3: Empty predictions")
+
+    gt = np.zeros((30, 30, 10), dtype=np.int32)
+    pred = np.zeros((30, 30, 10), dtype=np.int32)
+
+    # Only GT regions, no predictions
+    gt[5:15, 5:15, 2:8] = 1
+    gt[20:25, 20:25, 2:8] = 2
+
+    return gt, pred
+
+
+def test_scenario_4_extra_predictions():
+    """Test case with more predictions than GT regions"""
+    print("Test 4: Extra predictions")
+
+    gt = np.zeros((40, 40, 10), dtype=np.int32)
+    pred = np.zeros((40, 40, 10), dtype=np.int32)
+
+    # GT regions
+    gt[5:15, 5:15, 2:8] = 1
+
+    # Multiple predictions
+    pred[6:16, 6:16, 3:9] = 1  # Close to GT
+    pred[20:25, 20:25, 3:9] = 2  # Far from GT
+    pred[30:35, 30:35, 3:9] = 3  # Even farther
+
+    return gt, pred
+
+
+def run_test_scenario(gt, pred, scenario_name):
+    """Run a test scenario and return results"""
+    print(f"\n{scenario_name}")
+    print(f"GT unique values: {np.unique(gt)}")
+    print(f"Pred unique values: {np.unique(pred)}")
+
+    try:
+        # Create components
+        matcher = RegionBasedMatching(cca_backend=CCABackend.scipy)
+        approximator = ConnectedComponentsInstanceApproximator()
+        semantic_pair = SemanticPair(prediction_arr=pred, reference_arr=gt)
+
+        # Run evaluation
+        result = panoptic_evaluate(
+            input_pair=semantic_pair,
+            instance_approximator=approximator,
+            instance_matcher=matcher,
+            instance_metrics=[Metric.DSC, Metric.IOU],
+            global_metrics=[Metric.DSC],
+            verbose=False,
+        )
+
+        print(f"✅ {scenario_name} successful!")
+        print(
+            f"  Pred instances: {result.num_pred_instances}, Ref instances: {result.num_ref_instances}"
+        )
+        print(f"  TP: {result.tp}, FP: {result.fp}, FN: {result.fn}")
+
+        # Check individual metrics if available
+        if hasattr(result, "list_metrics") and result.list_metrics:
+            for metric, values in result.list_metrics.items():
+                if values:  # Only print if there are values
+                    avg_val = np.mean(values) if values else 0
+                    print(f"  {metric}: avg={avg_val:.3f}, values={len(values)}")
+
+        return True
+
+    except Exception as e:
+        print(f"❌ {scenario_name} failed: {e}")
+        import traceback
+
+        traceback.print_exc()
+        return False
+
+
+def main():
+    """Run all test scenarios"""
+    print("🧪 Running comprehensive RegionBasedMatching tests...")
+
+    scenarios = [
+        (test_scenario_1_basic, "Test 1: Basic non-overlapping"),
+        (test_scenario_2_overlapping, "Test 2: Overlapping predictions"),
+        (test_scenario_3_empty_prediction, "Test 3: Empty predictions"),
+        (test_scenario_4_extra_predictions, "Test 4: Extra predictions"),
+    ]
+
+    results = []
+    for scenario_func, name in scenarios:
+        gt, pred = scenario_func()
+        success = run_test_scenario(gt, pred, name)
+        results.append(success)
+
+    # Summary
+    passed = sum(results)
+    total = len(results)
+    print(f"\n📊 Test Summary: {passed}/{total} scenarios passed")
+
+    if passed == total:
+        print("🎉 All comprehensive tests passed!")
+        return True
+    else:
+        print("💥 Some tests failed!")
+        return False
+
+
+if __name__ == "__main__":
+    main()
diff --git a/unit_tests/test_region_integration.py b/unit_tests/test_region_integration.py
new file mode 100644
index 0000000..3b0a5d4
--- /dev/null
+++ b/unit_tests/test_region_integration.py
@@ -0,0 +1,103 @@
+#!/usr/bin/env python3
+"""
+Integration test for RegionBasedMatching with full panoptic evaluation
+"""
+
+import numpy as np
+from panoptica.panoptica_evaluator import panoptic_evaluate
+from panoptica.instance_matcher import RegionBasedMatching
+from panoptica.instance_approximator import ConnectedComponentsInstanceApproximator
+from panoptica.metrics import Metric
+from panoptica.utils.constants import CCABackend
+from panoptica.utils.processing_pair import SemanticPair
+
+
+def create_test_data():
+    """Create simple test data with ground truth and prediction instances"""
+    # Create a simple 3D volume with 2 GT regions
+    gt = np.zeros((50, 50, 20), dtype=np.int32)
+    pred = np.zeros((50, 50, 20), dtype=np.int32)
+
+    # GT region 1: cube in corner
+    gt[10:20, 10:20, 5:15] = 1
+
+    # GT region 2: cube in opposite corner
+    gt[30:40, 30:40, 5:15] = 2
+
+    # Prediction region 1: slightly offset from GT region 1
+    pred[12:22, 12:22, 6:16] = 1
+
+    # Prediction region 2: different location, should map to closest GT region
+    pred[25:35, 25:35, 6:16] = 2
+
+    return gt, pred
+
+
+def test_region_integration():
+    """Test RegionBasedMatching with full panoptic evaluation"""
+    print("Testing RegionBasedMatching with panoptic_evaluate...")
+
+    # Create test data
+    gt, pred = create_test_data()
+
+    print(f"GT shape: {gt.shape}, unique values: {np.unique(gt)}")
+    print(f"Pred shape: {pred.shape}, unique values: {np.unique(pred)}")
+
+    # Create region-based matcher
+    matcher = RegionBasedMatching(cca_backend=CCABackend.scipy)
+
+    # Create instance approximator
+    approximator = ConnectedComponentsInstanceApproximator()
+
+    try:
+        # Create semantic pair
+        semantic_pair = SemanticPair(prediction_arr=pred, reference_arr=gt)
+
+        # Run panoptic evaluation
+        result = panoptic_evaluate(
+            input_pair=semantic_pair,
+            instance_approximator=approximator,
+            instance_matcher=matcher,
+            instance_metrics=[Metric.DSC, Metric.IOU],
+            global_metrics=[Metric.DSC],
+            verbose=True,
+        )
+
+        print(f"\n✅ Integration test successful!")
+        print(f"Number of prediction instances: {result.num_pred_instances}")
+        print(f"Number of reference instances: {result.num_ref_instances}")
+        print(f"TP: {result.tp}")
+        print(f"FP: {result.fp}")
+        print(f"FN: {result.fn}")
+        print(f"Precision: {result.prec}")
+        print(f"Recall: {result.rec}")
+        print(f"RQ: {result.rq}")
+
+        # Check if metrics are NaN as expected for region-based matching
+        if np.isnan(result.tp):
+            print("✅ Count metrics correctly set to NaN for region-based matching")
+        else:
+            print("⚠️  Expected TP to be NaN for region-based matching")
+
+        # Check individual instance metrics
+        if hasattr(result, "list_metrics") and result.list_metrics:
+            print(f"\nInstance metrics:")
+            for metric, values in result.list_metrics.items():
+                print(f"  {metric}: {values}")
+
+        return True
+
+    except Exception as e:
+        print(f"❌ Error during integration test: {e}")
+        import traceback
+
+        traceback.print_exc()
+        return False
+
+
+if __name__ == "__main__":
+    success = test_region_integration()
+    if success:
+        print("\n🎉 All integration tests passed!")
+    else:
+        print("\n💥 Integration test failed!")
diff --git a/unit_tests/test_region_matching.py b/unit_tests/test_region_matching.py
new file mode 100644
index 0000000..332b522
--- /dev/null
+++ b/unit_tests/test_region_matching.py
@@ -0,0 +1,78 @@
+#!/usr/bin/env python3
+"""
+Test script for the RegionBasedMatching implementation
+"""
+
+import numpy as np
+from panoptica.instance_matcher import RegionBasedMatching
+from panoptica.utils.processing_pair import UnmatchedInstancePair
+from panoptica.utils.constants import CCABackend
+
+
+def create_test_data():
+    """Create simple test data with ground truth and prediction instances"""
+    # Create a simple 3D volume with 2 GT regions
+    gt = np.zeros((50, 50, 20), dtype=np.int32)
+    pred = np.zeros((50, 50, 20), dtype=np.int32)
+
+    # GT region 1: cube in corner
+    gt[10:20, 10:20, 5:15] = 1
+
+    # GT region 2: cube in opposite corner
+    gt[30:40, 30:40, 5:15] = 2
+
+    # Prediction region 1: slightly offset from GT region 1
+    pred[12:22, 12:22, 6:16] = 1
+
+    # Prediction region 2: different location, should map to closest GT region
+    pred[25:35, 25:35, 6:16] = 2
+
+    return gt, pred
+
+
+def test_region_based_matching():
+    """Test the RegionBasedMatching algorithm"""
+    print("Testing RegionBasedMatching...")
+
+    # Create test data
+    gt, pred = create_test_data()
+
+    # Create unmatched instance pair
+    unmatched_pair = UnmatchedInstancePair(prediction_arr=pred, reference_arr=gt)
+
+    print(f"Ground truth labels: {unmatched_pair.ref_labels}")
+    print(f"Prediction labels: {unmatched_pair.pred_labels}")
+
+    # Create region-based matcher
+    matcher = RegionBasedMatching(cca_backend=CCABackend.scipy)
+
+    # Perform matching
+    try:
+        labelmap = matcher._match_instances(unmatched_pair)
+
+        print(f"Matching successful!")
+        print(f"Label map: {labelmap.get_one_to_one_dictionary()}")
+
+        # Create matched instance pair
+        matched_pair = matcher.match_instances(unmatched_pair)
+
+        print(f"Matched instances: {matched_pair.matched_instances}")
+        print(f"Prediction instances: {matched_pair.n_prediction_instance}")
+        print(f"Reference instances: {matched_pair.n_reference_instance}")
+
+        return True
+
+    except Exception as e:
+        print(f"Error during matching: {e}")
+        import traceback
+
+        traceback.print_exc()
+        return False
+
+
+if __name__ == "__main__":
+    success = test_region_based_matching()
+    if success:
+        print("\n✅ Region-based matching test passed!")
+    else:
+        print("\n❌ Region-based matching test failed!")