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primary topic: Tools for multimodal atlases: bridging morphology and gene expression

Tools for multimodal atlases: bridging morphology and gene expression
type: Article
abstract: Maps combine different types of data, from a number of different sources, into the uniform grid of their coordinate system. They are invaluable resources as they allow the connections between data to be understood in their spatial context. We have been making biological maps for decades of all kinds of systems - for example, model organisms like Drosophila melanogaster and Caenorhabditis elegans have large atlases of neuronal cell types available. These large multimodal atlases (i.e. datasets that combine multiple data sources into one coordinate system) tend to undergo a similar ‘lifecycle’. First, a standard coordinate system is formed, followed by collection of the required datasets. These are then integrated into the common coordinate system, before they are analysed, and finally shared as a resource to the biological community. Electron microscopy (EM) offers many advantages when integrated into atlases of this kind. Firstly, it can achieve very high resolution, making it ideal for visualising small features like the fine structure of different organelles. It also provides the full spatial context of a tissue - allowing the locations and orientations of cells to be understood in a comprehensive manner. This comes at the cost of a number of challenges though. For one, EM is quite low throughput, meaning that often only a single sample can be imaged, or only small regions of a sample. Also, EM data can be extremely large (many terabytes in size) making it difficult to store, analyse, and share with other researchers. In my thesis, I aim to ease the integration of large-scale volume EM into multimodal atlases at various points within this lifecycle. First, at the acquisition stage, I look at increasing the speed, ease and precision of targeted EM acquisition. I develop two different methods - one focused on trimming resin-embedded blocks with an ultramicrotome, and the other with a Serial Block Face Scanning Electron Microscope (SBEM). Both these methods are provi…
date: 2022
author list: authors
type: EPrint
type: DoctoralThesisEPrint
is part of: repository
has document: Tools for multimodal atlases: bridging morphology and gene expression (PDF)
has document: Tools for multimodal atlases: bridging morphology and gene expression (Other)
subject: 500 Naturwissenschaften und Mathematik
subject: 570 Biowissenschaften, Biologie

Tools for multimodal atlases: bridging morphology and gene expression (PDF)
type: Document
has file: KimberlyMeechan_thesis.pdf
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Kimberly Meechan
type: Person
given name: Kimberly
family name: Meechan

Tools for multimodal atlases: bridging morphology and gene expression (Other)
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Tools for multimodal atlases: bridging morphology and gene expression (Other)
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Tools for multimodal atlases: bridging morphology and gene expression (Other)
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Tools for multimodal atlases: bridging morphology and gene expression (Other)
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Tools for multimodal atlases: bridging morphology and gene expression (Other)
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primary topic: Tools for multimodal atlases: bridging morphology and gene expression

500 Naturwissenschaften und Mathematik
type: Concept
preferred label: 500 Natural sciences and mathematics @en

570 Biowissenschaften, Biologie
type: Concept
preferred label: 570 Life sciences @en