Stitching of raw 2-photon tomography tiles and basic pre-processing were done using StitchIt.
Visualising of the full-resolution data was done with MaSIV and cell tracing with
MaSIV's neurite tracer plugin.
Registration of the traced neurite trees to the Allen Atlas was conducted using ARA Tools,
which just coordinates calls to Elastix via a MATLAB wrapper.
The quality of the registration was assessed using Lasagna.
Additional MATLAB tools for interacting with the Allen API are available from AllenBrainAPI. Code for analyses in the paper are at HanSingleCell (and related virus library data file).