SegmentPuzzler (GitHub) is a segmentation tool based on Supervoxels for 2D and 3D data written in C++. Very useful to merge and proofread segmentations.

Executables semi-available: Windows (Installer & Portable), Mac (M1 and Intel-based), AppImage for Linux (CentOS 7 and Ubuntu 22.04 tested)

Collection of Jupyter notebooks (GitHub) I've created as an introduction to both programming and image analysis in Python. Used in parts in exercises/tutoring for (applied) physics, engineering, and biology students. Includes links to be run online on Binder.

GUI for the deep learning-based segmentation and tracking of tunneling nanotubes (TNTs) in 2D+T data (GitHub). Comes with video tutorials, 1-click downloader & setup for models/weights, and versions for Linux and Windows. Based on a thesis by Gregor Stief I supervised at the University of Freiburg. Utilises nnU-Net for segmentation and TrackMate for tracking and analysis.