Serial two-photon tomography (STPT) of the brain through bi-channel image registration and deep learning segmentation (BIRDS)

We have developed an open-source software called BIRDS (bi-channel image
registration and deep learning segmentation) for the mapping and analysis
of 3D microscopy data and applied this to the mouse brain. The BIRDS
pipeline includes image pre-processing, bi-channel registration, automatic
annotation, creation of a 3D digital frame, high-resolution visualization,
and expandable quantitative analysis. This new bi-channel registration
algorithm is adaptive to various types of whole-brain data from different
microscopy platforms and shows dramatically improved registration
accuracy. Additionally, as this platform combines registration with neural
networks, its improved function relative to other platforms lies in the
fact that the registration procedure can readily provide training data for
network construction, while the trained neural network can efficiently
segment incomplete/defective brain data that is otherwise difficult to
register. Our software is thus optimized to enable either minute-timescale
registration-based segmentation of cross-modality, whole-brain datasets or
real-time inference-based image segmentation of various brain regions of
interest. Jobs can be easily submitted and implemented via a Fiji plugin
that can be adapted to most computing environments.