Power to the People: Addressing Big Data Challenges in Neuroscience by Creating a New Cadre of Citizen Neuroscientists

Roskams, Jane; Popović, Zoran

doi:10.1016/j.neuron.2016.10.045

Cited by 34 publications

(24 citation statements)

References 16 publications

(13 reference statements)

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“…Images were used to generate an automated reconstruction of the neuron using TReMAP (Zhou 2016). Alternatively, initial reconstructions were created manually using the reconstruction software PyKNOSSOS (Ariadne-service) or the citizen neuroscience game Mozak (Mosak.science) 64 . Automated or manually-initiated reconstructions were then extensively manually corrected and curated using a range of tools (e.g., virtual finger, polyline) in the Mozak extension (Zoran Popovic, Center for Game Science, University of Washington) of Terafly tools 65,66 in Vaa3D.…”

Section: Methodsmentioning

confidence: 99%

Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons

Berg

Sorensen

Ting

et al. 2020

Preprint

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The neocortex is disproportionately expanded in human compared to mouse, both in its total volume relative to subcortical structures and in the proportion occupied by supragranular layers that selectively make connections within the cortex and other telencephalic structures. Single-cell transcriptomic analyses of human and mouse cortex show an increased diversity of glutamatergic neuron types in supragranular cortex in human and pronounced gradients as a function of cortical depth. To probe the functional and anatomical correlates of this transcriptomic diversity, we describe a robust Patch-seq platform using neurosurgically-resected human tissues. We characterize the morphological and physiological properties of five transcriptomically defined human glutamatergic supragranular neuron types. Three of these types have properties that are specialized compared to the more homogeneous properties of transcriptomically defined homologous mouse neuron types. The two remaining supragranular neuron types, located exclusively in deep layer 3, do not have clear mouse homologues in supragranular cortex but are transcriptionally most similar to deep layer mouse intratelencephalic-projecting neuron types. Furthermore, we reveal the transcriptomic types in deep layer 3 that express high levels of non-phosphorylated heavy chain neurofilament protein that label long-range neurons known to be selectively depleted in Alzheimer’s disease. Together, these results demonstrate the power of transcriptomic cell type classification, provide a mechanistic underpinning for increased complexity of cortical function in human cortical evolution, and implicate discrete transcriptomic cell types as selectively vulnerable in disease.

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Section: Methodsmentioning

confidence: 99%

Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons

Berg

Sorensen

Ting

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Images were used to generate an automated reconstruction of the neuron using TReMAP (Zhou et al, 2016). Alternatively, reconstructions were created manually using the reconstruction software PyKNOSSOS (Ariadne-service) or the citizen neuroscience game Mozak (Mosak.science) (Roskams and Popović, 2016). Automated or manually-initiated reconstructions were then extensively manually corrected and curated using a range of tools (e.g., virtual finger, polyline) in the Mozak extension (Zoran Popovic, Center for Game Science, University of Washington) of Terafly tools (Peng et al, 2014;Bria et al, 2016) in Vaa3D.…”

Section: Morphological Reconstructionmentioning

confidence: 99%

Toward an integrated classification of neuronal cell types: morphoelectric and transcriptomic characterization of individual GABAergic cortical neurons

Gouwens

Sorensen²,

Baftizadeh³

et al. 2020

Preprint

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Neurons are frequently classified into distinct groups or cell types on the basis of structural, physiological, or genetic attributes. To better constrain the definition of neuronal cell types, we characterized the transcriptomes and intrinsic physiological properties of over 3,700 GABAergic mouse visual cortical neurons and reconstructed the local morphologies of 350 of those neurons. We found that most transcriptomic types (t-types) occupy specific laminar positions within mouse visual cortex, and many of those t-types exhibit consistent electrophysiological and morphological features. We observed that these properties could vary continuously between ttypes, which limited the ability to predict specific t-types from other data modalities. Despite that, the data support the presence of at least 20 interneuron met-types that have congruent morphological, electrophysiological, and transcriptomic properties.

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“…Despite the initial difficulties, attempts in these subdomains have continued to evolve, productively seeding subsequent developments. Citizen Science crowdsourcing may also provide a suitable alternative model 22 , opening the prospect of creating a community of curators. Our specific training protocol of neuroscience and bioinformatics students, piloted as a project-specific intern-ship program, gradually expanded over the years into a formal academic course.…”

Section: Lessons Learnedmentioning

confidence: 99%

Win–win data sharing in neuroscience

et al. 2017

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Power to the People: Addressing Big Data Challenges in Neuroscience by Creating a New Cadre of Citizen Neuroscientists

Cited by 34 publications

References 16 publications

Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons

Human cortical expansion involves diversification and specialization of supragranular intratelencephalic-projecting neurons

Toward an integrated classification of neuronal cell types: morphoelectric and transcriptomic characterization of individual GABAergic cortical neurons

Win–win data sharing in neuroscience

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