A Nix overlay containing various medical imaging packages, mostly from MICe or BIC-MNI, which have not been merged to Nixpkgs. A Git commit of this repository and of the upstream package set gives you a declarative way to completely specify your software dependencies down to base C libraries. Some HPC systems now provide Nix, and many others support Singularity containers, which you can build from a Nix derivation (similar to the Docker instructions in the manual).

A few things are missing, currently mostly visualization software such as Display, Register, ITK-snap, etc.

See the manual for usage instructions.

We may in future publish a recommended package set for medical imaging. Also, we are currently experimenting with publishing a binary cache at mouse-imaging-centre.cachix.org, but this is not automatically updated yet.

Of course, we welcome contributions including packages and bug reports.