  Despite the increased brilliance of the new generation synchrotron sources,
there is still a challenge with high-resolution scanning of very thick and
absorbing samples, such as the whole mouse brain stained with heavy elements,
and, extending further, brains of primates. Samples are typically cut into
smaller parts, to ensure a sufficient X-ray transmission, and scanned
separately. Compared to the standard tomography setup where the sample would be
cut into many pillars, the laminographic geometry operates with slab-shaped
sections significantly reducing the number of sample parts to be prepared, the
cutting damage and data stitching problems. In this work, we present a
laminography pipeline for imaging large samples (> 1 cm) at micrometer
resolution. The implementation includes a low-cost instrument setup installed
at the 2-BM micro-CT beamline of the Advanced Photon Source (APS).
Additionally, we present sample mounting, scanning techniques, data stitching
procedures, a fast reconstruction algorithm with low computational complexity,
and accelerated reconstruction on multi-GPU systems for processing large-scale
datasets. The applicability of the whole laminography pipeline was demonstrated
with imaging 4 sequential slabs throughout the entire mouse brain sample
stained with osmium, in total generating approximately 12TB of raw data for
reconstruction.
