The Brain/MINDS Marmoset Connectivity Atlas: exploring bidirectional tracing and tractography in the same stereotaxic space

Abstract

We report on the implementation and features of the Brain/MINDS Marmoset Connectivity Atlas, BMCA, a new resource that provides access to anterograde neuronal tracer data in the prefrontal cortex of a marmoset brain. Neuronal tracers combined with fluorescence microscopy are a key technology for the systematic mapping of structural brain connectivity. We selected the prefrontal cortex for mapping due to its important role in higher brain functions. This work introduces the BMCA standard image preprocessing pipeline and tools for exploring and reviewing the data. We developed the BMCA-Explorer, which is an online image viewer designed for data exploration. Unlike other existing image explorers, it visualizes the data of different individuals in a common reference space at an unprecedented high resolution, facilitating comparative studies. To foster the integration with other marmoset brain image databases and cross-species comparisons, we added fiber tractography data from diffusion MRI, retrograde neural tracer data from the Marmoset Brain Connectivity Atlas project, and tools to map image data between marmoset and the human brain image space. This version of BMCA allows direct comparison between the results of 52 anterograde and 164 retrograde tracer injections in the cortex of the marmoset.

Local and long-distance organization of prefrontal cortex circuits in the marmoset brain

“…1C, D). Registration fidelity to the common template space 24 was estimated to be 100-200 μm (Fig. S1A; see STAR Methods), which enabled reliable automatic anatomical annotations (Fig.…”

“…To facilitate 3D-3D registration between optically-based and MRI-based volumes, we built a standard reference image for a marmoset brain based on iteratively averaged Ch1 images 24 . We call this 50 μm-isocubic 3D image as the “STPT template.” To allow multimodal data integration, the initial averaging step was performed using BMA2019 Ex Vivo (Space 2), which is a 100 μm isocubic reference image based on a population average of 25 ex vivo MRI (T2) contrasts 72 .…”

“…The details of the image processing pipeline are described elsewhere 24,71 . Briefly, the raw images in the three channels were stitched after background correction.…”

“…To facilitate 3D-3D registration between optically-based and MRI-based volumes, we built a standard reference image for a marmoset brain based on iteratively averaged Ch1 images 24 . We call this 50 µm-isocubic 3D image as the "STPT template."…”

“…We also mapped the topographic organization of PFC connectivity to multiple regions of association cortex, in a pattern similar but not identical to that revealed by stimulation-fMRI mapping of macaque lateral PFC 23 . Our datasets are freely accessible (https://dataportal.brainminds.jp/; see also 24 ) and add to a growing collection of publicly available marmoset neuroscience-related datasets 25 .…”