Visualization and Quantification for Interactive Analysis of Neural Connectivity in <i>Drosophila</i>

Swoboda, Nicolas; Moosburner, J.; Brückner, Stefan; Yu, Jinxin; Dickson, Barry J.; Bühler, Katja

doi:10.1111/cgf.12792

Cited by 4 publications

(3 citation statements)

References 23 publications

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“…This rule states that proximity between Neurons increases their chance of forming synapses. Swoboda et al [SMB * 14, SMB * 17] build on this assumption by proposing a tool that studies connectivity by visually analyzing Neuron arborization overlaps. Since displaying all branches of the overlap directly in 3D would lead to a cluttered visualization, they only render glyphs (i.e., small dots color‐coding the amount of overlap).…”

Section: Segmentationmentioning

confidence: 99%

A Survey of Visualization and Analysis in High‐Resolution Connectomics

Beyer

Troidl

Boorboor³

et al. 2022

Computer Graphics Forum

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The field of connectomics aims to reconstruct the wiring diagram of Neurons and synapses to enable new insights into the workings of the brain. Reconstructing and analyzing the Neuronal connectivity, however, relies on many individual steps, starting from high‐resolution data acquisition to automated segmentation, proofreading, interactive data exploration, and circuit analysis. All of these steps have to handle large and complex datasets and rely on or benefit from integrated visualization methods. In this state‐of‐the‐art report, we describe visualization methods that can be applied throughout the connectomics pipeline, from data acquisition to circuit analysis. We first define the different steps of the pipeline and focus on how visualization is currently integrated into these steps. We also survey open science initiatives in connectomics, including usable open‐source tools and publicly available datasets. Finally, we discuss open challenges and possible future directions of this exciting research field.

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Section: Segmentationmentioning

confidence: 99%

A Survey of Visualization and Analysis in High‐Resolution Connectomics

Beyer

Troidl

Boorboor³

et al. 2022

Computer Graphics Forum

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“…Bruckner et al [BSG*09] proposed a system for visual inspection of volume data of fruit fly brains acquired through confocal microscopy. Given the availability of whole brain connectivity data of fruit flies, recently various efforts have been carried out to create interactive systems for connectivity analysis [SBS*13,SMB*17]. By contrast, we focus here on serial section electron microscopy images at nanometric resolution, since they are able to reveal intracellular details that are fundamental to understand neuro‐energetic processes [LPS14].…”

Section: Related Workmentioning

confidence: 99%

Interactive Volumetric Visual Analysis of Glycogen‐derived Energy Absorption in Nanometric Brain Structures

Agus

Calì

Al-Awami

et al. 2019

Computer Graphics Forum

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Digital acquisition and processing techniques are changing the way neuroscience investigation is carried out. Emerging applications range from statistical analysis on image stacks to complex connectomics visual analysis tools targeted to develop and test hypotheses of brain development and activity. In this work, we focus on neuroenergetics, a field where neuroscientists analyze nanoscale brain morphology and relate energy consumption to glucose storage in form of glycogen granules. In order to facilitate the understanding of neuroenergetic mechanisms, we propose a novel customized pipeline for the visual analysis of nanometric‐level reconstructions based on electron microscopy image data. Our framework supports analysis tasks by combining i) a scalable volume visualization architecture able to selectively render image stacks and corresponding labelled data, ii) a method for highlighting distance‐based energy absorption probabilities in form of glow maps, and iii) a hybrid connectivitybased and absorption‐based interactive layout representation able to support queries for selective analysis of areas of interest and potential activity within the segmented datasets. This working pipeline is currently used in a variety of studies in the neuroenergetics domain. Here, we discuss a test case in which the framework was successfully used by domain scientists for the analysis of aging effects on glycogen metabolism, extracting knowledge from a series of nanoscale brain stacks of rodents somatosensory cortex.

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“…They conclude that the best results are achieved using a combination of line coloring and intersection glyph display. Swoboda et al (2017) make heavy use of abstraction in the information and interaction design of their neuronal atlas interface. In collaboration with artists, they propose a highly reduced spatial visualization in order to avoid visual clutter.…”

Section: Advanced Visualization Techniquesmentioning

confidence: 99%

Towards Advanced Interactive Visualization for Virtual Atlases

Smit

Brückner

2019

Advances in Experimental Medicine and Biology

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An atlas is generally defined as a bound collection of tables, charts or illustrations describing a phenomenon. In an anatomical atlas for example, a collection of representative illustrations and text describes anatomy for the purpose of communicating anatomical knowledge. The atlas serves as reference frame for comparing and integrating data from different sources by spatially or semantically relating collections of drawings, imaging data, and/or text. In the field of medical image processing, atlas information is often constructed from a collection of regions of interest, which are based on medical images that are annotated by domain experts. Such an atlas may be employed for example for automatic segmentation of medical imaging data. The combination of interactive visualization techniques with atlas information opens up new possibilities for content creation, curation, and navigation in virtual atlases. With interactive visualization of atlas information, students are able to inspect and explore anatomical atlases in ways that were not possible with the traditional method of presenting anatomical atlases in book format, such as viewing the illustrations from other viewpoints. With advanced interaction techniques, it becomes possible to query the data that forms the basis for the atlas, thus empowering researchers to access a wealth of information in new ways. So far, atlas-based visualization has been employed for mainly medical education, as well as biological research. In this survey, we provide an overview of current digital biomedical atlas tasks and applications and summarize relevant visualization techniques. We discuss recent approaches for providing nextgeneration visual interfaces to navigate atlas data that go beyond common textbased search and hierarchical lists. Finally, we reflect on open challenges and opportunities for the next steps in interactive atlas visualization.

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Visualization and Quantification for Interactive Analysis of Neural Connectivity in Drosophila

Cited by 4 publications

References 23 publications

A Survey of Visualization and Analysis in High‐Resolution Connectomics

A Survey of Visualization and Analysis in High‐Resolution Connectomics

Interactive Volumetric Visual Analysis of Glycogen‐derived Energy Absorption in Nanometric Brain Structures

Towards Advanced Interactive Visualization for Virtual Atlases

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