MTNeuro: A Benchmark for Evaluating Representations of Brain Structure Across Multiple Levels of AbstractionDownload PDF

Published: 17 Sept 2022, Last Modified: 23 May 2023NeurIPS 2022 Datasets and Benchmarks Readers: Everyone
Keywords: self-supervised learning, visual reasoning, neuroanatomy, semantic segmentation, multi-scale context aggregation
TL;DR: A multi-task, multi-scale benchmark for evaluating representations of volumetric brain data
Abstract: There are multiple scales of abstraction from which we can describe the same image, depending on whether we are focusing on fine-grained details or a more global attribute of the image. In brain mapping, learning to automatically parse images to build representations of both small-scale features (e.g., the presence of cells or blood vessels) and global properties of an image (e.g., which brain region the image comes from) is a crucial and open challenge. However, most existing datasets and benchmarks for neuroanatomy consider only a single downstream task at a time. To bridge this gap, we introduce a new dataset, annotations, and multiple downstream tasks that provide diverse ways to readout information about brain structure and architecture from the same image. Our multi-task neuroimaging benchmark (MTNeuro) is built on volumetric, micrometer-resolution X-ray microtomography images spanning a large thalamocortical section of mouse brain, encompassing multiple cortical and subcortical regions. We generated a number of different prediction challenges and evaluated several supervised and self-supervised models for brain-region prediction and pixel-level semantic segmentation of microstructures. Our experiments not only highlight the rich heterogeneity of this dataset, but also provide insights into how self-supervised approaches can be used to learn representations that capture multiple attributes of a single image and perform well on a variety of downstream tasks. Datasets, code, and pre-trained baseline models are provided at:
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License: The dataset is released under the CC by 4.0 license ( The code is released under the MIT license (
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