Introduction: Quantitative maps of neurotransmitter receptor densities are important tools for characterising the molecular organisation of the brain and key for understanding normal and pathologic brain function and behaviour. We describe a novel pipeline that can reconstruct 3D cortical volumes for data sets of multiple different types of 2D post-mortem histological sections, including autoradiographs acquired with different ligands, cell body stained sections, and myelin stained sections. The reconstructed data in this study were primarily composed of autoradiographs and hence the application of our pipeline will allow for the creation of the first ever set of ultra-high resolution 3D atlases for 20 different neurotransmitter binding sites in 3 complete human brains and and in 3 hemispheres of 3 different macaque brains.
Methods: The reconstruction pipeline is composed of 4 major stages: 1) semi-automated cropping of the histological sections 2) inter-section 2D alignment, 3) iterative multi-resolution 3D volumetric alignment followed by 2D section-wise alignment of sections to a reference structural brain image (e.g., the donor’s T1 MRI or stereotaxic template), 4) morphologically-informed cortical surface-based interpolation to estimate missing pixel intensities between sections acquired for a given ligand or stain. To demonstrate the efficacy of the pipeline, it was applied to autoradiograph sections measuring 20 different receptor binding sites from a single human hemisphere to reconstruct 20 volumes at 250x250x250μm3, each representing binding densities for a different neurotransmitter receptor. Additionally, as a proof-of-principle that the pipeline can be used to reconstruct non-human brains, the pipeline was used to reconstruct myelin- and cell-body stained sections and GABAA associated benzodiazepine (GABAA/BZ) binding sites from autoradiographs acquired from a macaque hemisphere.
Results: The Dice score of the alignment between histological sections and the reference structural volume was 0.91±.10. Overall the interpolation accuracy of the receptor binding densities was an average of 98% versus pixel intensities measured in the raw autoradiographs. Missing autoradiograph densities were estimated using surface-based interpolation and had a correlation of r2=0.98±0.001 between true and interpolated pixel intensities.
Discussion: The methods presented here make possible the reconstruction of extremely challenging data sets of sparsely sampled, heterogenous histological sections from severely deformed brains. Hitherto such reconstruction had not been possible and valuable histological data sets, such those used here, had remained unreconstructed. Moreover, we show that these methods, while designed for data acquired from human brains, generalizes to other species, namely macaques, and do not strictly require a reference structural volume from the same brain as the sections were acquired. This has allowed us to produce a data set of multiple neurotransmitter receptor atlases for human and non-human primate brains. The methods we describe now allow us to create a set of novel and unparalleled 3D receptor atlases in MNI152 space for the neuroscience community.