A Visual Interface for Exploring Hypotheses About Neural Circuits

Vohra, Sumit Kumar; Harth, Philipp; Isoe, Yasuko; Bahl, Armin; Fotowat, Haleh; Engert, Florian; Hege, Hans‐Christian; Baum, Daniel

doi:10.1109/tvcg.2023.3243668

Cited by 4 publications

(3 citation statements)

References 46 publications

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“…To address this issue, we extended the existing FishExplorer platform (https://fishexplorer.zib.de) containing the larval zebrafish brain (Z-brain) atlas (https://fishexplorer.zib.de/zebrafish/lm) that has been established and used to study neural circuits (Randlett et al 2015; Vohra et al 2023), to allow for the seamless incorporation of a larval medaka brain (M-brain). To compare brain anatomical regions among different fish species, we parceled each brain into the corresponding mutually exclusive and comprehensively exhaustive (MECE) regions, which cover the whole brain without overlaps and without gaps.…”

Section: Mainmentioning

confidence: 99%

Multi-species community platform for comparative neuroscience in teleost fish

Vohra,

Herrera,

Tavhelidse-Suck

et al. 2024

Preprint

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Studying neural mechanisms in complementary model organisms from different ecological niches in the same animal class can leverage the comparative brain analysis at the cellular level. To advance such a direction, we developed a unified brain atlas platform and specialized tools that allowed us to quantitatively compare neural structures in two teleost larvae, medaka (Oryzias latipes) and zebrafish (Danio rerio). Leveraging this quantitative approach we found that most brain regions are similar but some subpopulations are unique in each species. Specifically, we confirmed the existence of a clear dorsal pallial region in the telencephalon in medaka lacking in zebrafish. Further, our approach allows for extraction of differentially expressed genes in both species, and for quantitative comparison of neural activity at cellular resolution. The web-based and interactive nature of this atlas platform will facilitate the teleost community's research and its easy extensibility will encourage contributions to its continuous expansion.

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Section: Mainmentioning

confidence: 99%

Multi-species community platform for comparative neuroscience in teleost fish

Vohra,

Herrera,

Tavhelidse-Suck

et al. 2024

Preprint

Self Cite

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“…The first digital atlas of the larval zebrafish brain, the virtual brain explorer (ViBE-Z), was built for 3 days post fertilization (DPF) larvae, a period in which larvae are fully transparent and many circuit elements are already established. 14 Using custom landmark alignment, elastic 16 Hildebrand et al 22 Vohra et al 23 Zebrafish Brain Browser 6 dpf Hundreds of labels (confocal), ∼294 brain regions (Z-Brain), and 3D visualization Marquart et al 17 Marquart et al 18 MapZebrain 6 dpf >700 labels (confocal), ∼70 brain regions, neuronal morphology and connectivity, and EM data Kunst et al 19 Svara et al 24 Shainer et al 21 MRI Atlas Adult High-resolution magnetic resonance histology and 53 brain regions Ullmann et al 25 AZBA Adult 10 labels (tissue clearing + lightsheet) and >200 brain regions Kenney et al 26 registration, and intensity correction algorithms, the authors assembled 17 co-registered labels from multiple fish in a standardized volume using confocal microscopy. Drawing from similar work in Drosophila, 15 this work established a standard framework for atlas building in the zebrafish, as multiple elements of this first iteration, such as the use of a second structural staining for alignment, manual segmentations of anatomical regions, and an open-access web portal, have been key elements of the subsequent resources.…”

Section: Atlases Of the Larval Zebrafish Brainmentioning

confidence: 99%

“…Given sufficiently detailed functional measurements, atlases can provide experimentalists with narrowed-down circuit hypotheses that account for the observed neuronal dynamics and behaviors. As these databases continue to grow, however, the manual interrogation of thousands of markers and reconstructed cells becomes very tedious, and efforts are underway to find optimal search algorithms and modeling frameworks to efficiently provide users with candidate circuit models 23 . Hypothetical circuits derived from atlases will then necessarily have to be confronted with functional and structural validations from, for instance, post-hoc screenings of molecular labels, 35 opsin-based optogenetics, 36 , 37 or viral-based retrograde tracing, 38 as the true connectivity or colocalization between markers can only be inferred experimentally.…”

Section: Perspectivesmentioning

confidence: 99%

Zebrafish brain atlases: a collective effort for a tiny vertebrate brain

Légaré,

Lemieux,

Desrosiers

et al. 2023

Neurophoton.

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In the past two decades, digital brain atlases have emerged as essential tools for sharing and integrating complex neuroscience datasets. Concurrently, the larval zebrafish has become a prominent vertebrate model offering a strategic compromise for brain size, complexity, transparency, optogenetic access, and behavior. We provide a brief overview of digital atlases recently developed for the larval zebrafish brain, intersecting neuroanatomical information, gene expression patterns, and connectivity. These atlases are becoming pivotal by centralizing large datasets while supporting the generation of circuit hypotheses as functional measurements can be registered into an atlas' standard coordinate system to interrogate its structural database. As challenges persist in mapping neural circuits and incorporating functional measurements into zebrafish atlases, we emphasize the importance of collaborative efforts and standardized protocols to expand these resources to crack the complex codes of neuronal activity guiding behavior in this tiny vertebrate brain.

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Vimo: Visual Analysis of Neuronal Connectivity Motifs

Troidl

Warchol

Choi

et al. 2022

Preprint

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Recent advances in high-resolution connectomics provide researchers access to accurate reconstructions of vast neuronal circuits and brain networks for the first time. Neuroscientists anticipate analyzing these networks to gain a better understanding of information processing in the brain. In particular, scientists are interested in identifying specific network motifs, i.e., repeating subgraphs of the larger brain network that are believed to be neuronal building blocks. To analyze these motifs, it is crucial to review instances of a motif in the brain network and then map the graph structure to the detailed 3D reconstructions of the involved neurons and synapses. We present Vimo, an interactive visual approach to analyze neuronal motifs and motif chains in large brain networks. Experts can sketch network motifs intuitively in a visual interface and specify structural properties of the involved neurons and synapses to query large connectomics datasets. Motif instances (MIs) can be explored in high-resolution 3D renderings of the involved neurons and synapses. To reduce visual clutter and simplify the analysis of MIs, we designed a continuous focus&context metaphor inspired by continuous visual abstractions that allows the user to transition from the highly-detailed rendering of the anatomical structure to views that emphasize the underlying motif structure and synaptic connectivity. Furthermore, Vimo supports the identification of motif chains where a motif is used repeatedly to form a longer synaptic chain. We evaluate Vimo in a user study with seven domain experts and an in-depth case study on motifs in the central complex (CX) of the fruit fly brain.

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A Visual Interface for Exploring Hypotheses About Neural Circuits

Cited by 4 publications

References 46 publications

Multi-species community platform for comparative neuroscience in teleost fish

Multi-species community platform for comparative neuroscience in teleost fish

Zebrafish brain atlases: a collective effort for a tiny vertebrate brain

Vimo: Visual Analysis of Neuronal Connectivity Motifs

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