Computing instance-wise segmentation quality metrics for 2D and 3D semantic- and instance segmentation maps.
The package provides 3 core modules:
- Instance Approximator
- Instance Matcher
- Panoptic Evaluator
To install the current release, you can simply run:
pip install panoptica
Although for many biomedical segmentation problems, an instance-wise evaluation is highly relevant and desirable, they are still addressed as semantic segmentation problems due to lack of appropriate instance labels.
Modules [1-3] can be used to obtain panoptic metrics of matched instances based on a semantic segmentation input.
It is a common issue that instance segementation outputs have good segmentations with mismatched labels.
For this case modules [2-3] can be utilized to match the instances and report panoptic metrics.
Ideally the input data already provides matched instances.
In this case module 3 can be used to directly report panoptic metrics without requiring any internal preprocessing.
Juypter notebook Tutorials are avalable for all use cases in our tutorials repo.
If you have used panoptica in your research, please cite us! The citation can be exported from: TODO