Sparse 4-D multi-spectral optical computed tomography for accurate quantification of voxel composition

这个项目是关于开发一种新型显微镜，称为多光谱吸收光学计算机断层扫描仪。从x射线计算机断层扫描（即所谓的CAT扫描仪，在20世纪七八十年代彻底改变了医学诊断）的发展开始，三维成像在现代医学和科学中无处不在。计算机断层扫描的原理被应用于多种领域，如化学工程中火焰的远程监测、埃及金字塔的寻墓（通过介子断层扫描）和辐射剂量的非侵入性测绘，以提供放射治疗的质量保证。光学计算机断层扫描-或“光学投影断层扫描”（OPT），作为生物显微镜中广泛使用的配置，已被称为-提供高质量的图像，在所谓的中尺度上特别有用，样品尺寸为厘米数量级，能够分辨小到5-10微米的细节。OPT的两种主要形式是可用的，发射和吸收断层扫描。这个项目是关于吸收层析成像，其中一束光照射在样品上，我们从穿过样品的光形成三维图像，从而测量由于样品中各种组织成分的光学吸收而透射光减少的量。不同波长的组织吸收程度不同。光学吸收光谱具有高度的独特性，可用于分离出组织的重要成分。这项技术通常用于传统的二维显微镜，目的是定位载玻片上含有不同类型组织的区域，这些组织被不同类型的化学物质“染色”，以使它们更明显，彼此之间更明显。测量是在（通常情况下，相对较少的）离散波长上进行的，并在称为“光谱分解”的过程中由计算机进行分析。为了使这个分解过程顺利进行，我们需要调整化学添加剂（污渍）的浓度，使它们在我们的相机可测量的范围内让适量的光通过。然而，对于我们用于癌症的3d动物模型来说，这种调整是非常困难的，因为在这些“造影剂”被输送到组织的过程中存在重大的未知因素。负责任的动物实验原则，包括减少使用的动物数量和改进技术，强烈主张开发“智能”读出系统，正如本项目所建议的那样，从使用的每只动物中获得最大价值。分解过程可能失败的第二个原因是，我们可能事先不知道待分解化合物的光谱是什么。一种令人兴奋的基于金纳米颗粒的新型造影剂家族，当它们被引入组织时，光谱会发生变化。这是不幸的，因为它阻碍了我们通过光谱分解精确测量纳米颗粒浓度的能力。近年来，人们对金纳米颗粒的兴趣激增，尤其是对其中一种被称为金纳米棒的亚型。这些纳米棒可以附着在各种分子上，这些分子可以识别体内癌症的特定特征，因此，我们希望通过准确测量纳米棒在组织中聚集的位置，我们可以检测并可能量化恶性组织的数量。本项目采用的数据采集和处理技术在OPT中是非常新颖的，它可以将需要采集的数据量减少约1 / 2。这一点非常重要，因为光谱OPT涉及非常大的数据集。我们的项目包括三个部分：(i)模拟和优化收购过程；（ii）建立新的显微镜；(3)在两个与癌症密切相关的问题上进行测试。

This project is about developing a new type of microscope called a multi-spectral absorption optical computed tomography scanner.Starting with the development of x-ray computed tomography - the so called CAT scanners that revolutionised medical diagnosis in the 1970's and '80s - three-dimensional imaging has become ubiquitous in modern medicine and science. Principles of computed tomography are employed in fields as diverse as remote monitoring of flames in chemical engineering, tomb-hunting in Egyptian pyramids (via muon tomography) and non-invasive mapping of radiation dose to provide quality assurance in radiotherapy treatments.Optical computed tomography - or "optical projection tomography" (OPT) as the configuration widely used in biological microscopy has come to be known - provides high quality images that are especially useful at the so-called mesoscale, with sample dimensions of the order of cm and able to resolve details as small as a 5-10 microns. Two principal forms of OPT are available, emission and absorption tomography. This project is concerned with absorption tomography, in which a beam of light shines on a sample and we form a 3-D image from the light that passes through the sample, thus measuring the amount by which the transmitted light decreases because of optical absorption by the various tissue components in the sample.Tissue absorption occurs to different degrees at different wavelengths. Optical absorption spectra are highly distinctive and may be used to separate out important components of tissue. This technique is routinely used in traditional 2-D microscopy in order to locate regions on the slide containing different types of tissue, which are "stained" with different types of chemical in order to make them more visible and more distinct from each other. Measurements are made at a (normally, relatively small) number of discrete wavelengths and analysed by computer in a process that is know as "spectral unmixing".In order for this unmixing process to work well, we need to adjust the concentrations the chemical additives (stains) such that they let through an appropriate amount of light in the range measureable by our camera. However, for the sorts of 3-D animal model that we use in cancer, this adjustment is very difficult to do, because there are significant unknowns in the processes by which these "contrast agents" are delivered to tissue. Principles of responsible animal experimentation, involving a reduction in the number of animals used and a refinement of techniques argue strongly for the development of a "smart" readout system, as suggested in this project, to gain maximum value from each animal used.A second reason for possible failures in the unmixing process is that we might not know in advance what the spectra of the compounds to be unmixed are. The spectra of an exciting new family of contrast agent, based on gold nanoparticles, can vary when they are introduced into tissue. This is unfortunate, as it hinders our ability to make accurate measurements of nanoparticle concentration via spectral unmixing. There has been an explosion of interest in gold nanoparticles in recent years, and particularly in one of the subtypes, known as gold nanorods. These can be attached to various molecules that recognise particular signatures of cancer within the body and, thus, the hope is that by measuring accurately where the nanorods congregate in tissue, we can detect and, perhaps, quantify the amount of malignant tissue.The data acquisition and processing technique used in this project is very new in OPT. It will reduce the amount of data that need to be acquired by a factor of approximately. This is extremely important because spectral OPT involves very large datasets. Our project consists of three parts: (i) simulate and optimise the acquisition process; (ii) build the new microscope; (iii) test it in two problems of great interest in cancer.