Mario Emmenlauer Dipl. Inf. Mario Emmenlauer
Biozentrum Basel
Klingelbergstrasse 50/70
CH-4056 Basel
Telephone (Office): +41-(0)61-26-72200
Skype: emmenlau
Email: mario.emmenlauer *

Scientific Interests

Biological and medical image processing and machine learning, registration of large scale image datasets, fusion, stitching, spine- and neuron-tracing. Platform-independant programming in C/C++, templates, compilers, CPU/GPU programming.


  • M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt.
    "Xuvtools: Free, fast and reliable stitching of large 3d datasets"
    Journal of Microscopy (2009) Vol 233 Issue 1 pp. 42--60 (doi:10.1111/j.1365-2818.2008.03094.x)
    Paper (on publisher site, free access) [pdf]

  • M. Emmenlauer, O. Ronneberger, H. Burkhardt, A. Ponti, P. Schwarb, R. Nitschke, and W. Driever.
    "XuvTools: Fast and reliable stitching of large 3D datasets"
    European Light Microscopy Initiative ELMI (2008)
    Poster [pdf]

  • M. Emmenlauer and O. Ronneberger and M. Temerinac and H. Burkhardt and A. Filippi and R. Nitschke and W. Driever
    "Fast Automatic Recombination of Multiple 3D Datasets for Large Volumes and High Dynamic Range (HDR)"
    49th Symposium of the Society for Histochemistry (2007)
    Poster [pdf]

  • Mario Emmenlauer
    "Feature- und Deformationsmodell-basierte Registrierung von 3D Volumendaten von Zebrafischen"
    Diploma thesis [pdf] [ps.gz], Diploma recital [pdf]



  • XuvTools: Free, Fast and Reliable Stitching of Large 3D Datasets
    XuvTools is a fully automatic software toolset for stitching very large 3D confocal microscope datasets (mosaics). Tiles have to be acquired without distortions, and need to have some overlap for the automatic placement to work. XuvTools is designed to be very fast and precise and to work without prior knowledge about recording positions (fully automatic).




Links, Software