Welcome to panoptica’s documentation!

PyPI version panoptica Documentation Status tests


Computing instance-wise segmentation quality metrics for 2D and 3D semantic- and instance segmentation maps.


The package provides three core modules:

  1. Instance Approximator: instance approximation algorithms to extract instances from semantic segmentation maps/model outputs.

  2. Instance Matcher: matches predicted instances with reference instances.

  3. Instance Evaluator: computes segmentation and detection quality metrics for pairs of predicted - and reference segmentation maps.



With a Python 3.10+ environment, you can install panoptica from pypi.org

pip install panoptica

Use cases and tutorials

For tutorials featuring various use cases, see: BrainLesion/tutorials/panoptica

Semantic Segmentation Input


Jupyter notebook tutorial

Although an instance-wise evaluation is highly relevant and desirable for many biomedical segmentation problems, they are still addressed as semantic segmentation problems due to the lack of appropriate instance labels.

This tutorial leverages all three modules of panoptica: instance approximation, -matching and -evaluation.

Unmatched Instances Input


Jupyter notebook tutorial

It is a common issue that instance segmentation outputs feature good outlines but mismatched instance labels. For this case, the matcher module can be utilized to match instances and the evaluator to report metrics.

Matched Instances Input


Jupyter notebook tutorial

If your predicted instances already match the reference instances, you can directly compute metrics using the evaluator module.


If you use panoptica in your research, please cite it to support the development!

Kofler, F., Möller, H., Buchner, J. A., de la Rosa, E., Ezhov, I., Rosier, M., Mekki, I., Shit, S., Negwer, M., Al-Maskari, R., Ertürk, A., Vinayahalingam, S., Isensee, F., Pati, S., Rueckert, D., Kirschke, J. S., Ehrlich, S. K., Reinke, A., Menze, B., Wiestler, B., & Piraud, M. (2023). Panoptica – instance-wise evaluation of 3D semantic and instance segmentation maps. arXiv preprint arXiv:2312.02608.

      title={Panoptica -- instance-wise evaluation of 3D semantic and instance segmentation maps},
      author={Florian Kofler and Hendrik Möller and Josef A. Buchner and Ezequiel de la Rosa and Ivan Ezhov and Marcel Rosier and Isra Mekki and Suprosanna Shit and Moritz Negwer and Rami Al-Maskari and Ali Ertürk and Shankeeth Vinayahalingam and Fabian Isensee and Sarthak Pati and Daniel Rueckert and Jan S. Kirschke and Stefan K. Ehrlich and Annika Reinke and Bjoern Menze and Benedikt Wiestler and Marie Piraud},

Indices and tables