I work on machine learning for biomedical and scientific imaging — instance segmentation, cell tracking, and the data infrastructure around them — in the Kainmueller Lab at the MDC Berlin.
| Repo | What it is |
|---|---|
| pycyz | Pure-Python reader for CytoSense .cyz flow cytometer files — no .NET runtime, no proprietary DLLs, standard library only. (Python, MIT) |
| DeepSPM | Reinforcement learning approach for autonomously acquiring and classifying data in multi-day Scanning Probe Microscopy experiments. _(Python) Communications Physics 2020 |
| Octree | Out-of-core octree implementation for visualizing large voxel datasets with GPU-based raycasting. (C++) |
| TreeHugger | Research project: tree growth via Lindenmayer systems with dynamic branch movement on a ~1m×2m multi-touch screen. (C++) |
| Shadow-Volume | Small shadow volume implementation. (C++) |
| Repo | What it is |
|---|---|
| PatchPerPix | Official implementation of the PatchPerPix instance segmentation method. _(Python, MIT) ECCV 2020 |
| fisbe | Project page for FISBe, a real-world benchmark dataset for instance segmentation of long-range thin filamentous structures → kainmueller-lab.github.io/fisbe CVPR 2024 |
| linajea | Cell tracking pipeline: from 3d+time light sheet data to extracted cell lineage tracks, via deep learning and ILP-based graph optimization. _(Python, MIT) Nature Biotechnology 2022, MICCAI 2022 |
| shift-equivariance | How Shift Equivariance Impacts Metric Learning for Instance Segmentation and What can go wrong with tile & stitch prediction ICCV 2021 |
| aqqua | Project page for AqQua, the Aquatic Life Foundation Project — quantifying life at scale in a changing world → kainmueller-lab.github.io/aqqua |
| evaluate-instance-segmentation | 2d/3d instance segmentation metrics with skeleton-based (clDice) matching and explicit false-merge / false-split attribution (Official implementation of the FISBe evaluation pipeline). (Python, MIT) |
| aux_cpv_loss | An auxiliary task for learning nuclei segmentation in 3d microscopy images. (Python, MIT) MIDL 2020 |
| AqQua-LatLon-to-Region | Determines the Longhurst Province for a given lat/lon coordinate. (Python, MIT) |