General instructions


In order to reconstruct your data yourself as well as access (view) the reconstructed data you need a DESY account. Ask your local contact if do not have a DESY account. The account should be created before the beamtime starts!

Reconstructions with Matlab

This is currently the standard reconstruction software for the P05 µCT setup.

  1. Use FastX or ssh -X to log in on a maxwell node (see External user account)
  2. In your maxwell home directory, clone matlab reco software

    git clone https://github.com/moosmann/matlab
  3. This will create a matlab folder in your home folder. Start matlab with the startscript provided with the reco software

    cd matlab
    ./startmatlab.sh
  4. In Matlab open matlab/experiments/p05/p05_reco.m
  5. Edit top section of the p05_reco.m script
  6. Run reco script


In order to acknowledge the work for the reconstruction software, please cite the following paper in your publications:

Moosmann, J. et al. "Time-lapse X-ray phase-contrast microtomography for in vivo imaging and analysis of morphogenesis", Nat. Protocols 9, 294-304 (2014)

DOI: 10.1038/nprot.2014.033