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A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images (BMC Bioinformatics 2012, 13:316), exploiting multi-level parallelism for stitching very large microscopy images (Frontiers in Neuroinformatics, 13, 2019).

Before using this software, you MUST accept the LICENSE.txt

Documentation, help and other info are available on our Github wiki at


  • Alessandro Bria (email: Post-doctoral Fellow at University of Cassino (Italy). Main developer.

  • Giulio Iannello (email: Full Professor at University Campus Bio-Medico of Rome (italy). Supervisor and co-developer.

  • Roberto Valenti (email: Software Developer at University Campus Bio-Medico of Rome (Italy). Co-developer.

Main features

  • designed for images exceeding the TeraByte size
  • fast and reliable 3D stitching based on a multi-MIP approach
  • typical memory requirement below 4 GB (8 at most)
  • 2D stitching (single slice images) supported
  • regular expression based matching for image file names
  • data subset selection
  • sparse data support
  • i/o plugin-based architecture
  • stitching of multi-channel images
  • support for big tiff files (> 4 GB)
  • HDF5-based formats
  • parallelization on multi-core platform
  • fast alignment computation on NVIDIA GPUs