Welcome to ZetaStitcher’s documentation!

ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.

Key features:

  • able to handle datasets as big as 1012 voxels

  • multichannel images

  • powerful and simple Python API to query arbitrary regions within the fused volume

How to install

On Ubuntu 20.04 LTS, run these commands:

sudo apt-get install python3-pip libgl1 libglib2.0-0
pip3 install zetastitcher

Docker image

To build a docker image with ZetaStitcher:

make docker

You can call the stitching commands using an ephemeral container like this:

docker run -it -v`pwd`:/home --rm zetastitcher stitch-align -h
docker run -it -v`pwd`:/home --rm zetastitcher stitch-fuse -h


Please read the documentation and follow the tutorial at this page:


This open source software code was developed in whole in the Human Brain Project, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No. 720270 and No. 785907 (Human Brain Project SGA1 and SGA2).

Co-funded by the European Union

Latest package

The latest built package can be downloaded from here (version 0.7.0.post1).