Pottslab

Pottslab — Multilabel image segmentation via the Potts model

Unsupervised multilabel image segmentation (colour, grayscale, multichannel) via the Potts model — also known as the piecewise-constant Mumford-Shah model or the ℓ⁰ gradient model. Solvers for 1-D denoising / step detection, 2-D image segmentation, and joint reconstruction-and-segmentation (deconvolution, Radon / MRI / PET).

Featured in the MATLAB Central Pick of the Week (2017).

Quickstart

Python (Rust core)

pip install pottslab

import numpy as np
from pottslab import min_l2_potts, min_l2_potts_2d

# 1-D: denoise / step-detect a noisy piecewise-constant signal
y = np.array([0., 0.1, 0.05, 1.05, 0.95, 1.1, 0.0])
u = min_l2_potts(y, gamma=0.5)

# 2-D: segment a vector-valued image (H, W, C)
img = np.random.rand(64, 64, 3)
seg = min_l2_potts_2d(img, gamma=0.3)

The Python package wraps a Rust extension built with PyO3 and maturin; algorithm crates live under src/, demos under demos_python/. See README_PYTHON.md for the full Python API, inverse-Potts / sparsity / Tikhonov variants, and performance figures.

MATLAB

The original MATLAB / Java reference implementation is in this same repository:

1. Run installPottslab.m to add the necessary folders to the MATLAB path.
2. For best performance, increase Java heap space in the MATLAB preferences (MATLAB → General → Java Heap Memory).
3. Run a demo from the Demos/ folder.

Troubleshooting

• OutOfMemoryException — Increase Java heap space in the MATLAB preferences.
• Undefined variable “pottslab” or class “pottslab.JavaTools.minL2Potts” — Run setPLJavaPath.m. You may also need to install Java 1.7 (see e.g. undocumentedmatlab.com).

Standalone (command line, plain image segmentation only)

java -jar pottslab-standalone.jar input output.png gamma

where gamma is a positive real number, e.g. 0.1 (thanks to fxtentacle).

Application examples

Segmentation of vector-valued images

• Supports vector-valued images (multispectral, feature images)
• Linear complexity in the number of channels
• Label-free: no label discretisation required

Left: A natural image. Right: Result using the Potts model.

Texture segmentation using high-dimensional curvelet-based feature vectors.

Used as the segmentation method in:

• A. Breger et al. Supervised learning and dimension reduction techniques for quantification of retinal fluid in optical coherence tomography images, Eye (2017).

Joint image reconstruction and segmentation

• Applicable to many imaging operators (convolution, Radon, MRI, PET, MPI) — only the proximal mapping is needed
• Supports vector-valued data
• Label-free: labels need not be chosen a priori

Left: Shepp-Logan phantom. Centre: Filtered backprojection from 7 angular projections. Right: Joint reconstruction and segmentation using the Potts model from 7 angular projections.

Denoising / step detection of jump-sparse signals

• L1 Potts model is robust to noise and to moderately blurred data
• Fast and exact solver for the L1 Potts model
• Approximative strategies for severely blurred data

Top: Noisy signal. Bottom: Minimiser of the Potts functional (ground truth in red).

Used as the step-detection algorithm in:

• A. Nord et al. Catch bond drives stator mechanosensitivity in the bacterial flagellar motor, PNAS, 2017.
• A. Szorkovszky et al. Assortative interactions revealed by sorting of animal groups, Animal Behaviour, 2018.

Plugins for image-analysis GUIs

Parts of Pottslab can be used without MATLAB as pure Java plugins:

• Icy plugin — interactive image segmentation based on Pottslab (Vasileios Angelopoulos).
• ImageJ plugin — ImageJ frontend for Pottslab (Michael Kaul).

How to cite

If you use this software, please cite the relevant paper(s) below. GitHub’s “Cite this repository” button on the repo page reads the version and date-released fields from CITATION.cff and renders BibTeX/APA.

References

• M. Storath, A. Weinmann, J. Frikel, M. Unser. Joint image reconstruction and segmentation using the Potts model, Inverse Problems, 2015.
• A. Weinmann, M. Storath. Iterative Potts and Blake-Zisserman minimization for the recovery of functions with discontinuities from indirect measurements, Proceedings of the Royal Society A, 471(2176), 2015.
• A. Weinmann, M. Storath, L. Demaret. The L1-Potts functional for robust jump-sparse reconstruction, SIAM Journal on Numerical Analysis, 2015.
• M. Storath, A. Weinmann. Fast partitioning of vector-valued images, SIAM Journal on Imaging Sciences, 2014.
• M. Storath, A. Weinmann, L. Demaret. Jump-sparse and sparse recovery using Potts functionals, IEEE Transactions on Signal Processing, 2014.

See also

Sibling projects from the same research program on variational methods for signal and image processing:

• L1TV — exact L1-TV regularisation of real- or circle-valued signals
• CSSD — cubic smoothing splines for signals with discontinuities
• MumfordShah2D — edge-preserving image restoration via the Mumford-Shah model
• CircleMedianFilter — fast median filtering for phase or orientation data
• DCEBE — bolus arrival time estimation for DCE-MRI signals

Related external projects:

• PALMS Image Segmentation — piecewise affine linear estimation.
• Higher order Mumford-Shah models — piecewise smooth signals.

License

Released under the MIT License. See LICENSE.

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Project history

The Python / Rust port of this codebase was generated from the original MATLAB / Java reference by a Claude coding agent in 2026. The agent also found and fixed an off-by-one bug in the weighted-median computation inside IndexedLinkedHistogram (in both the new Rust port and the original Java). See PORTED_BY.md for full attribution and the porting plan.

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