ViMO - Visual Analysis of Neuronal Connectivity Motifs

Troidl, Jakob; Warchol, Simon; Choi, Jinhan; Matelsky, Jordan; Dhanyasi, Nagaraju; Wang, Xueying; Wester, Brock; Wei, Donglai; Lichtman, Jeff W.; Pfister, Hanspeter; Beyer, Johanna

doi:10.1109/tvcg.2023.3327388

Cited by 2 publications

(1 citation statement)

References 44 publications

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“…Many visualization tools are tailored to the life sciences. For instance, genomics [41,42,56], connectomics [1,4,70], and histology [27,32,67,73] have utilized visualizations. Imaging data, in particular, is well-suited for visualizations due to the inherent visual nature of the data [72].…”

Section: Cell Biology Visualizationsmentioning

confidence: 99%

Aardvark: Composite Visualizations of Trees, Time-Series, and Images

Lange,

Judson-Torres,

Zangle

et al. 2024

Preprint

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How do cancer cells grow, divide, proliferate and die? How do drugs influence these processes? These are difficult questions that we can attempt to answer with a combination of time-series microscopy experiments, classification algorithms, and data visualization. However, collecting this type of data and applying algorithms to segment and track cells and construct lineages of proliferation is error-prone; and identifying the errors can be challenging since it often requires cross-checking multiple data types. Similarly, analyzing and communicating the results necessitates synthesizing different data types into a single narrative.State-of-the-art visualization methods for such data use independent line charts, tree diagrams, and images in separate views. However, this spatial separation requires the viewer of these charts to combine the relevant pieces of data in memory.To simplify this challenging task, we describe design principles for weaving cell images, time-series data, and tree data into a cohesive visualization. Our design principles are based on choosing a primary data type that drives the layout and integrates the other data types into that layout. We then introduce Aardvark, a system that uses these principles to implement novel visualization techniques. Based on Aardvark, we demonstrate the utility of each of these approaches for discovery, communication, and data debugging in a series of case studies.

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Section: Cell Biology Visualizationsmentioning

confidence: 99%

Aardvark: Composite Visualizations of Trees, Time-Series, and Images

Lange,

Judson-Torres,

Zangle

et al. 2024

Preprint

View full text Add to dashboard Cite

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Beyond neurons: computer vision methods for analysis of morphologically complex astrocytes

Syed,

Youssef,

Schober

et al. 2024

Front. Comput. Sci.

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The study of the geometric organization of biological tissues has a rich history in the literature. However, the geometry and architecture of individual cells within tissues has traditionally relied upon manual or indirect measures of shape. Such rudimentary measures are largely a result of challenges associated with acquiring high resolution images of cells and cellular components, as well as a lack of computational approaches to analyze large volumes of high-resolution data. This is especially true with brain tissue, which is composed of a complex array of cells. Here we review computational tools that have been applied to unravel the cellular nanoarchitecture of astrocytes, a type of brain cell that is increasingly being shown to be essential for brain function. Astrocytes are among the most structurally complex and functionally diverse cells in the mammalian body and are essential partner cells of neurons. Light microscopy does not allow adequate resolution of astrocyte morphology, however, large-scale serial electron microscopy data, which provides nanometer resolution 3D models, is enabling the visualization of the fine, convoluted structure of astrocytes. Application of computer vision methods to the resulting nanoscale 3D models is helping reveal the geometry and organizing principles of astrocytes, but a complete understanding of astrocyte structure and its functional implications will require further adaptation of existing computational tools, as well as development of new approaches.

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ViMO - Visual Analysis of Neuronal Connectivity Motifs

Cited by 2 publications

References 44 publications

Aardvark: Composite Visualizations of Trees, Time-Series, and Images

Aardvark: Composite Visualizations of Trees, Time-Series, and Images

Beyond neurons: computer vision methods for analysis of morphologically complex astrocytes

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