Ram, K. | bioRxiv Science

bioRxiv2018

A High-throughput Neurohistological Pipeline for Brain-Wide Mesoscale Connectivity Mapping of the Common Marmoset

Understanding the connectivity architecture of entire vertebrate brains is a fundamental but difficult task. MRI based methods offer whole brain coverage, but remain indirect in the approach to connectivity mapping. Recent progress has been made in directly mapping whole-brain connectivity architecture in the mouse at the mesoscopic scale. The basic approach uses tracer injections systematically placed on a grid of locations spanning the brain and computational analysis of the resulting whole brain data sets. Scaling this approach to bigger primate brains poses nontrivial technical challenges. Here we present an integrated neurohistological pipeline as well as a grid-based tracer injection strategy for systematic mesoscale connectivity mapping in the common Marmoset (Callithrix jacchus). Individual brains are sectioned into [~]1700 20{micro}m sections using the tape transfer technique, permitting high quality 3D reconstruction of a series of histochemical stains (Nissl, myelin) interleaved with tracer labelled sections. Combining the resulting 3D volumes, containing informative cytoarchitectonic markers, with in-vivo and ex-vivo MRI, and using an integrated computational pipeline, we are able to overcome the significant individual variation exhibited by Marmosets to obtain routine and high quality maps to a common atlas framework. This will facilitate the systematic assembly of a mesoscale connectivity matrix together with unprecedented 3D reconstructions of brain-wide projection patterns in a primate brain. While component instruments or protocols may be available from previous work, we believe that this is the first detailed systems-level presentation of the methodology required for high-throughput neuroanatomy in a model primate.

neuroscience↗

bioRxiv2018

High precision automated detection of labelednuclei in terabyte-scale whole-brain volumetricimage data of mouse

There is a need in modern neuroscience for accurate and automated image processing techniques for analyzing the large volume of neuroanatomical data. For e.g., the use of light microscopy to image whole mouse brains in a mesoscopic scale produces individual neuroanatomical data volumes in the TerraByte range.. A fundamental task involves the detection and quantification of objects of a given type, e.g. neuronal nuclei or somata, in whole mouse brains. Traditionally this quantification is performed by human visual inspection with high accuracy, that is not scalable.. When state-of-the-art CNN and SVM-based methods are used to solve this classification problem, they achieve accuracy levels between 85 - 92%. However, higher rates of precision and recall, close to that of humans are necessary. In this paper, we describe an unsupervised, iterative algorithm, which provides a high close to human performance for a specific problem of broad interest, i.e. detection of Green Fluorescent Protein labeled nuclei in whole mouse brains. The algorithm judiciously combines classical computer vision (CV) techniques and is focused on the complex problem of decomposing strong overlapped objects (nuclei). Our proposed iterative method uses features detected on ridge lines over distance transformation and an arc based iterative spatial-filling method to solve the problem. We demonstrate our results on two whole mouse brain data sets of Gigabyte resolution and compare it with manual annotation of the brains. Our results show that an aptly designed CV algorithm with classical feature extractors when tailored to this problem of interest achieves near-ideal human-like performance. Quantitative analysis, when compared with the manually annotated ground truth, reveals that our approach performs better on whole mouse brain scans than general purpose machine learning (including deep CNN) methods.

neuroscience↗