MAPPING THE BRAIN: Sub-100nm resolution, large volume X-ray connectomics with near-field multislice ptychography

绘制大脑图谱：亚 100 纳米分辨率、大体积 X 射线连接组学和近场多层叠层成像

基本信息

批准号：
BB/X003221/1
负责人：
ANDREW MICHAEL MAIDEN
金额：
$ 20.7万
依托单位：
University of Sheffield
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2023
资助国家：
英国
起止时间：
2023 至无数据
项目状态：
未结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FX003221%2F1
关键词：
MAPPING BRAIN Sub 100nm resolution

项目摘要

Mapping the thousands of connections between individual neurons in the brain, a field called connectomics, is critical to our understanding of the mechanisms behind neurodegenerative conditions, such as autism and schizophrenia, and the brain's complex responses to stimuli, such as images, smells and sounds. For many decades, electron microscopy (EM) has been the dominant imaging technique in connectomics, and recent advances in EM methods now enable 3D imaging of regions of the brain up to several hundred micrometres cubed in volume. This is sufficient to capture the entire nervous systems of invertebrates or small vertebrate animals, such as larvae. Unfortunately, these EM techniques work by shaving very thin slices from the sample to be imaged one by one. This means they require months to years of data acquisition and processing times, whilst the slicing process itself is destructive and highly error-prone. Thus, while providing the highest resolution, using EM alone it is difficult to obtain wider contextual information, such as the identity of neurons that are linked together by the synapses visible in the EM 3D images. This project aims to develop a bridging method that can provide correlative, non-destructive imaging of brain tissue at sub-100nm resolution, to target and contextualise EM connectomics. Advanced forms of synchrotron X-ray microscopy already go some way toward providing this contextual information, and advantageously, the penetrative power of X-rays means these methods can image large sample volumes quickly and without destructive slicing; the problem is that sample volume and resolution must trade off against one another - larger, thicker samples scatter the X-ray beam leading to a rapid falloff in image resolution. Current state-of-the-art X-ray microscopy can achieve a resolution of approximately 100nm over a 200 micron thick sample; this project will develop a new 3D X-ray tool to image brain tissue at sub-100nm resolution over a cubic millimetre volume. Until recently, the ideas we explore in this project would have been impossible given the computing resources required. Today however, phenomenal advances in computer hardware, especially parallel computing on Graphic Processing Units (GPUs), mean processes that required many hours to run a decade ago are now possible in close to real time. This is transforming the way Researchers think about the role and potential of computing in microscopy. Our work in this project is based on one such transformative technique called ptychography, which uses iterative algorithms to reconstruct an image of an object from diffraction data captured by a very simple, lens-free optical system. Essentially ptychography replaces the lenses in an X-ray microscope with code. The field of ptychography has grown exponentially over the past decade and dedicated ptychography beamlines are now coming online at most synchrotrons around the world. The UK is at the forefront of this research, with a strong track record in algorithm development and novel experimental approaches. Our project will complement these on-going efforts and ensure ptychography remains an active, competitive topic within the UK, and that the UK remains a world-leader in this exciting and rapidly growing field.Our Programme brings together Sheffield University, the Diamond Light Source and the Crick Institute in a new and exciting collaboration. The Investigative team holds expertise at every step of the technique development journey, from optical bench proof of principle, through implementation at the synchrotron to cutting edge, high impact application studies in collaboration with the brain specialists at the Crick Institute.

绘制大脑中单个神经元之间的数千个连接（一个称为连接组学的领域）对于我们理解神经退行性疾病（例如自闭症和精神分裂症）背后的机制以及大脑对刺激（例如图像、气味和声音）的复杂反应至关重要。几十年来，电子显微镜 (EM) 一直是连接组学领域的主导成像技术，而 EM 方法的最新进展现在可以对体积达数百微米立方的大脑区域进行 3D 成像。这足以捕获无脊椎动物或小型脊椎动物（例如幼虫）的整个神经系统。不幸的是，这些电磁技术的工作原理是从待成像的样品中切下非常薄的切片，然后一张一张地进行成像。这意味着它们需要数月至数年的数据采集和处理时间，而切片过程本身具有破坏性且极易出错。因此，在提供最高分辨率的同时，单独使用 EM 很难获得更广泛的上下文信息，例如通过 EM 3D 图像中可见的突触连接在一起的神经元的身份。该项目旨在开发一种桥接方法，能够以亚 100 nm 分辨率提供脑组织的相关、非破坏性成像，以定位和背景化 EM 连接组学。先进形式的同步加速器 X 射线显微镜已经在提供这种背景信息方面取得了一定的进展，有利的是，X 射线的穿透力意味着这些方法可以快速对大样本量进行成像，而无需破坏性切片；问题在于样品体积和分辨率必须相互权衡 - 较大、较厚的样品会散射 X 射线束，导致图像分辨率迅速下降。目前最先进的 X 射线显微镜可以在 200 微米厚的样品上实现约 100 纳米的分辨率；该项目将开发一种新的 3D X 射线工具，以亚 100 纳米分辨率对立方毫米体积的脑组织进行成像。直到最近，考虑到所需的计算资源，我们在这个项目中探索的想法都是不可能的。然而，如今，计算机硬件的显着进步，尤其是图形处理单元 (GPU) 上的并行计算，意味着十年前需要数小时才能运行的流程现在可以接近实时地运行。这正在改变研究人员思考计算在显微镜中的作用和潜力的方式。我们在这个项目中的工作基于一种称为叠层摄影术的变革技术，该技术使用迭代算法根据非常简单的无透镜光学系统捕获的衍射数据来重建物体的图像。本质上，叠印术用代码取代了 X 射线显微镜中的镜头。过去十年来，叠层记录技术领域呈指数级增长，专用叠层记录光束线现已在世界各地的大多数同步加速器上上线。英国处于这项研究的前沿，在算法开发和新颖的实验方法方面拥有良好的记录。我们的项目将补充这些正在进行的努力，并确保叠印术在英国仍然是一个活跃的、有竞争力的话题，并且英国在这个令人兴奋和快速发展的领域仍然处于世界领先地位。我们的项目汇集了谢菲尔德大学、钻石光源与克里克研究所进行了一项新的、令人兴奋的合作。研究团队在技术开发过程的每一步都拥有专业知识，从光具座原理证明，到同步加速器的实施，再到与克里克研究所的大脑专家合作进行尖端、高影响力的应用研究。