CC-Metrics

Every Component Counts: Rethinking the Measure of Success for Medical Semantic Segmentation in Multi-Instance Segmentation Tasks

Description

Traditional metrics often fail to adequately capture the performance of models in multi-instance segmentation scenarios, particularly when dealing with heterogeneous structures of varying sizes. CC-Metrics addresses this by:

1. Identifying individual connected components in ground-truth labels
2. Creating Voronoi regions around each component to define its territory
3. Mapping predictions within each Voronoi region to the corresponding ground-truth component
4. Computing standard metrics on these mapped regions for more granular assessment

Recent News from new release (v0.0.3)

The latest version includes performance improvements:

• Faster Voronoi computation: New compute_voronoi_regions_fast implementation using single EDT computation
• Memory-efficient processing: Automatic cropping to regions of interest reduces memory footprint
• Caching no longer needed: Fast computation is now efficient enough that caching is typically unnecessary

Below is an example visualization of the Voronoi-based mapping process:

For more details, you can read the full paper here.

Table of Contents

• Description
• Installation
• How to Use CC-Metrics
  • Basic Usage
  • Supported Metrics
  • Metric Aggregation
  • Caching Mechanism
  • Advanced Examples
• FAQ
• Contributing
• Citation
• License

Installation

You may install CC-Metrics simply by running

pip install CCMetrics

Another option is the editable installation directly from the source code:

Prerequisites

• Python 3.8+
• PyTorch 1.8+
• MONAI 0.9+

git clone https://github.com/alexanderjaus/CC-Metrics.git
cd CC-Metrics
pip install -e .

GPU Acceleration

CC-Metrics includes optional GPU-accelerated preprocessing for the Voronoi space separation to speed up large-volume evaluations.

• Requirements: NVIDIA GPU, CUDA 12.x, a CUDA-enabled PyTorch, and a matching CuPy build (cupy-cuda12x).
• Install from PyPI with extras: pip install "CCMetrics[gpu]" (or CCMetrics[all]).
• Install from source with extras: pip install -e .[gpu].

Usage example:

from CCMetrics import CCDiceMetricGPU
cc_dice_gpu = CCDiceMetricGPU(cc_reduction="patient", use_caching=False)

Notes on CPU/GPU parity: CPU and GPU paths share the same algorithm (single-EDT Voronoi + MONAI metrics). Minor numerical differences can occur due to library tie-breaking when assigning equidistant background voxels to components. In our checks across 441 volumes, aggregated CC‑Dice differences were very small (patient-wise mean diff ~1e-5; per-component mean diff ~5e-5), with rare worst-case patient differences up to ~3.5e-3. If exact agreement is required, run the CPU metric path.

How to Use CC-Metrics

CC-Metrics defines wrappers around MONAI's Cumulative metrics to enable per-component evaluation.

Basic Usage

Here's a simple example using the CCDiceMetric:

from CCMetrics import CCDiceMetric
import torch

# Create the metric with desired parameters
cc_dice = CCDiceMetric(
    cc_reduction="patient",  # Aggregation mode
    use_caching=False        # Recommended: use fast computation (v0.0.3+)
)

# Create sample prediction and ground truth tensors
# Tensors must be in shape (B, C, D, H, W) where:
# B = batch size (currently only B=1 is supported)
# C = number of channels (must be 2: background and foreground)
# D, H, W = depth, height, width of the volumetric data
y = torch.zeros((1, 2, 64, 64, 64))
y_hat = torch.zeros((1, 2, 64, 64, 64))

# Create two ground truth components
y[0, 1, 20:25, 20:25, 20:25] = 1  # Component 1
y[0, 1, 40:45, 40:45, 40:45] = 1  # Component 2
y[0, 0] = 1 - y[0, 1]  # Background

# Create prediction (slightly offset from ground truth)
y_hat[0, 1, 21:26, 21:26, 21:26] = 1  # Prediction for component 1
y_hat[0, 1, 41:46, 39:44, 41:46] = 1  # Prediction for component 2
y_hat[0, 0] = 1 - y_hat[0, 1]  # Background

# Compute the metric
cc_dice(y_pred=y_hat, y=y)

# Get the results
patient_wise_results = cc_dice.cc_aggregate()
#tensor([0.5120])

print(f"CC-Dice score: {patient_wise_results.mean().item()}")

# You can change the scheme during aggregation
component_wise_results = cc_dice.cc_aggregate(mode="overall")
#tensor([0.5120, 0.5120])

Supported Metrics

CC-Metrics includes the following metrics, all derived from MONAI:

• CCDiceMetric: Component-wise Dice coefficient

  CCDiceMetric()
  

• CCHausdorffDistanceMetric: Component-wise Hausdorff distance

  CCHausdorffDistanceMetric(metric_worst_score=30)
  

• CCHausdorffDistance95Metric: Component-wise 95th percentile Hausdorff distance

  CCHausdorffDistance95Metric(metric_worst_score=30)
  

• CCSurfaceDistanceMetric: Component-wise average surface distance

  CCSurfaceDistanceMetric(metric_worst_score=30)
  

• CCSurfaceDiceMetric: Component-wise Surface Dice score

  CCSurfaceDiceMetric(class_thresholds=[1])
  

  This class needs the additional parameter class_thresholds, a list of class-specific thresholds. The thresholds relate to the acceptable amount of deviation in the segmentation boundary in pixels. Each threshold needs to be a finite, non-negative number. More details here

Metric Aggregation

The CCBaseMetric class supports two types of metric aggregation modes:

1. Patient-Level Aggregation (patient):

   • Computes the mean metric score for each patient by aggregating all connected components within the patient
   • Returns a list of mean scores, one for each patient
   • Useful when you want to evaluate performance on a per-patient basis

2. Overall Aggregation (overall):

   • Treats all connected components across all patients equally
   • Aggregates the metric scores for all components into a single list
   • Useful when you want to evaluate performance across all components regardless of patient boundaries

The aggregation mode can be specified using the cc_aggregate method, with the default mode being patient.

# Patient-level aggregation (default)
patient_results = cc_dice.cc_aggregate(mode="patient")

# Overall aggregation
overall_results = cc_dice.cc_aggregate(mode="overall")

Caching Mechanism

CC-Metrics requires the computation of a generalized Voronoi diagram which serves as the mapping mechanism between predictions and ground-truth. As the separation of the image space only depends on the ground-truth, the mapping can be cached and reused between intermediate evaluations or across metrics.

Recommended Approach (v0.0.3+)

We now recommend disabling caching and relying on the fast computation instead. The new compute_voronoi_regions_fast function is so efficient that the overhead of caching often outweighs the benefits:

cc_dice = CCDiceMetric(
    cc_reduction="patient",
    use_caching=False  # Recommended: use fast computation instead
)

Performance Comparison

Starting with v0.0.3, the Voronoi computation has been significantly optimized. The new compute_voronoi_regions_fast function provides:

• Faster computation through single EDT operations
• Reduced memory overhead
• Better scalability for large volumes with many components
• Improved flexibility

Legacy Caching Support

For backward compatibility, caching is still supported but generally not recommended:

# Legacy approach - not recommended for most use cases
cc_dice = CCDiceMetric(use_caching=True, caching_dir="/path/to/cache")

Advanced Examples

Performance Optimizations

CC-Metrics v0.0.3+ includes several performance improvements that make it more efficient for large-scale evaluations:

Automatic Region Cropping: The library now automatically crops to the minimal bounding box containing each connected component and its Voronoi region, significantly reducing memory usage and computation time for sparse segmentations.

Improved Voronoi Computation: The new compute_voronoi_regions_fast function uses a more efficient single EDT (Euclidean Distance Transform) approach, eliminating the need for KDTree-based computations.

Memory Management: Enhanced garbage collection and tensor operation optimization reduce memory leaks and improve performance for batch processing.

Evaluating Multiple Metrics on the Same Data

from CCMetrics import CCDiceMetric, CCSurfaceDiceMetric, CCHausdorffDistance95Metric
import torch

# Create sample data
y = torch.zeros((1, 2, 64, 64, 64))
y_hat = torch.zeros((1, 2, 64, 64, 64))

# Set up components (simplified example)
y[0, 1, 20:25, 20:25, 20:25] = 1
y[0, 0] = 1 - y[0, 1]
y_hat[0, 1, 21:26, 21:26, 21:26] = 1
y_hat[0, 0] = 1 - y_hat[0, 1]

# Define shared settings (caching no longer recommended)
use_fast_computation = True

# Initialize metrics
metrics = {
    "dice": CCDiceMetric(use_caching=False),
    "surface_dice": CCSurfaceDiceMetric(use_caching=False, class_thresholds=[1]),
    "hd95": CCHausdorffDistance95Metric(use_caching=False, metric_worst_score=30)
}

# Compute all metrics
results = {}
for name, metric in metrics.items():
    metric(y_pred=y_hat, y=y)
    results[name] = metric.cc_aggregate().mean().item()

print(f"Results: {results}")

FAQ

Q: What's new in version 2.0?

A: Version 2.0 includes significant performance improvements:

• New optimized Voronoi computation algorithm (compute_voronoi_regions_fast)
• Automatic region cropping to reduce memory usage
• Enhanced memory management and tensor operations
• Overall 2-5x speedup in typical use cases compared to previous version
• Caching is no longer recommended - the fast computation is now efficient enough that caching overhead often exceeds benefits

Q: Should I use caching?

A: No, we recommend disabling caching. The new compute_voronoi_regions_fast function is so efficient that the I/O overhead of caching typically outweighs any performance benefits. Simply set use_caching=False when initializing metrics.

Q: Why use CC-Metrics instead of traditional metrics?

A: Traditional metrics like Dice can be misleading in multi-instance segmentation tasks. CC-Metrics provides a more granular assessment of performance by evaluating each component separately, making it particularly valuable for medical imaging tasks with multiple structures of varying sizes.

Q: How does CC-Metrics handle false negatives (ground truth components with no matching predictions)?

A: CC-Metrics assigns the worst score to false negative regions, ensuring they appropriately penalize the overall performance score.

Q: How does CC-Metrics handle false positives (predicted components with no matching ground truth)?

A: CC-Metrics evaluates locally thus positive predictions reduce the scores in the region into which they fall.

Q: Is multi-class segmentation supported?

A: Currently, CC-Metrics only supports binary segmentation (background and foreground). Multi-class support is planned for future releases.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

Citation

If you make use of this project in your work, please cite the CC-Metrics paper:

@article{jaus2024every,
  title={Every Component Counts: Rethinking the Measure of Success for Medical Semantic Segmentation in Multi-Instance Segmentation Tasks},
  author={Jaus, Alexander and Seibold, Constantin Marc and Rei{\ss}, Simon and Marinov, Zdravko and Li, Keyi and Ye, Zeling and Krieg, Stefan and Kleesiek, Jens and Stiefelhagen, Rainer},
  booktitle={Proceedings of the AAAI Conference on Artificial Intelligence},
  volume={39},
  number={4},
  pages={3904--3912},
  year={2025}
}

License

This project is licensed under the Apache 2.0 License.