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（一个称为连接组学领域）对于我们对神经退行性疾病背后的机制（例如自闭症和精神分裂症）以及大脑对刺激的复杂反应（例如图像，气味和声音）至关重要。数十年来，电子显微镜（EM）一直是连接组中的主要成像技术，而EM方法的最新进展现在可以使大脑区域的3D成像可达数百微米，该区域的体积数量数量数量为数百微米。这足以捕获无脊椎动物或小脊椎动物（例如幼虫）的整个神经系统。不幸的是，这些EM技术是通过从样品中刮去非常薄的切片来进行成像的。这意味着他们需要数月到数年的数据获取和处理时间，而切片过程本身具有破坏性且高度容易出错。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，例如神经元的身份，这些神经元与EM 3D图像中可见的突触相连。该项目旨在开发一种可以在100nm分辨率下对脑组织提供相关的，无损的成像的桥接方法，以靶向和上下文与EM连接组。同步加速器X射线显微镜的高级形式已经在提供此上下文信息方面进行了某种方式，并且有利地，X射线的穿透力意味着这些方法可以快速成像大型样品量，而无需破坏性切片。问题在于，样品体积和分辨率必须相互贸易 - 较大，较厚的样品散布X射线梁，导致图像分辨率迅速下降。当前的最新X射线显微镜可以在200微米厚的样品上实现约100nm的分辨率；该项目将开发出一种新的3D X射线工具，以在立方毫米体积上以低于100nm的分辨率对脑组织进行图像。直到最近，考虑到所需的计算资源，我们在该项目中探讨的想法将是不可能的。但是，如今，计算机硬件的惊人进步，尤其是在图形处理单元（GPU）上的并行计算，平均过程需要十年前进行数小时的运行，现在可以实时实时。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。我们在该项目中的工作基于一种称为PtyChography的变革性技术，该技术使用迭代算法从一个非常简单，无镜头的光学系统捕获的衍射数据中重建对象的图像。基本上，Ptychography用代码代替了X射线显微镜中的镜头。在过去的十年中，PtyChography领域的发展呈指数增长，而专用的Ptychography Beainslines现在在世界各地的大多数同步基因上都在线上。英国处于这项研究的最前沿，在算法开发和新颖的实验方法方面具有良好的记录。我们的项目将补充这些持续的努力，并确保Ptychography在英国内仍然是一个积极的竞争性话题，并且英国在这个令人兴奋且快速发展的领域中仍然是世界领导者。我们的计划将谢菲尔德大学，钻石光源和克里克研究所汇集在一起，进行了新的和令人兴奋的合作。调查团队在技术开发旅程的每个步骤中都拥有专业知识，从光学基准证明到在同步加速器上实施到最前沿，与Crick Institute的大脑专家合作，高影响力应用研究。