Rembrandt Bakker
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View article: Multi-scale spiking network model of human cerebral cortex
Multi-scale spiking network model of human cerebral cortex Open
Although the structure of cortical networks provides the necessary substrate for their neuronal activity, the structure alone does not suffice to understand the activity. Leveraging the increasing availability of human data, we developed a…
View article: Beyond Barrels: Diverse Thalamocortical Projection Motifs in the Mouse Ventral Posterior Complex
Beyond Barrels: Diverse Thalamocortical Projection Motifs in the Mouse Ventral Posterior Complex Open
Thalamocortical pathways from the rodent ventral posterior (VP) thalamic complex to the somatosensory cerebral cortex areas are a key model in modern neuroscience. However, beyond the intensively studied projection from medial VP (VPM) to …
View article: MEBRAINS 1.0: A new population-based macaque atlas
MEBRAINS 1.0: A new population-based macaque atlas Open
Due to their fundamental relevance, the number of anatomical macaque brain templates is constantly growing. Novel templates aim to alleviate limitations of previously published atlases and offer the foundation to integrate multiscale multi…
View article: Translating single-neuron axonal reconstructions into meso-scale connectivity statistics in the mouse somatosensory thalamus
Translating single-neuron axonal reconstructions into meso-scale connectivity statistics in the mouse somatosensory thalamus Open
Characterizing the connectomic and morphological diversity of thalamic neurons is key for better understanding how the thalamus relays sensory inputs to the cortex. The recent public release of complete single-neuron morphological reconstr…
View article: Analyzing Thalamocortical Tract-Tracing Experiments in a Common Reference Space
Analyzing Thalamocortical Tract-Tracing Experiments in a Common Reference Space Open
View article: Precise registration of axonal morphologies obtained from sections to a common reference space
Precise registration of axonal morphologies obtained from sections to a common reference space Open
We present a strategy to register manually traced neuronal morphologies to a reference atlas, with the final goal to publish the aligned neurons in the EBRAINS knowledge-graph, visualize them in the interactive atlas viewer and compare the…
View article: MEBRAINS 1.0: a new population-based macaque atlas
MEBRAINS 1.0: a new population-based macaque atlas Open
Due to their fundamental relevance, the number of anatomical macaque brain templates is constantly growing. Novel templates aim to alleviate limitations of previously published atlases and offer the foundation to integrate multiscale multi…
View article: Reconstructing axons from sectioned brains through alignment and stitching
Reconstructing axons from sectioned brains through alignment and stitching Open
Since the turn of this century, new and powerful cell labeling techniques have allowed the consistent and complete labeling of axonal arborizations of individual long range projection neurons (LRPNs) in mouse (Furuta et al, 2001). The pros…
View article: Multi-Scale Spiking Network Model of Human Cerebral Cortex
Multi-Scale Spiking Network Model of Human Cerebral Cortex Open
Although the structure of cortical networks provides the necessary substrate for their neuronal activity, the structure alone does not suffice to understand it. Leveraging the increasing availability of human data, we developed a multi-sca…
View article: Investigating the Impact of Outsourcing on IT Flexibility
Investigating the Impact of Outsourcing on IT Flexibility Open
Modern healthcare organizations try to leverage their IT infrastructures to enhance the efficiency of processes and the quality of patient services. The flexibility of the IT infrastructure is a critical factor in the process of establishi…
View article: Bringing Anatomical Information into Neuronal Network Models
Bringing Anatomical Information into Neuronal Network Models Open
View article: AB0930 URATE INDUCED PRIMING OF HUMAN MONOCYTES IS MEDIATED VIA THE TGF-Β PATHWAY
AB0930 URATE INDUCED PRIMING OF HUMAN MONOCYTES IS MEDIATED VIA THE TGF-Β PATHWAY Open
View article: Prediction of a Cell-Class-Specific Mouse Mesoconnectome Using Gene Expression Data
Prediction of a Cell-Class-Specific Mouse Mesoconnectome Using Gene Expression Data Open
View article: Correction to: Multi-scale account of the network structure of macaque visual cortex
Correction to: Multi-scale account of the network structure of macaque visual cortex Open
View article: Prediction of a cell-type specific mouse mesoconnectome using gene expression data
Prediction of a cell-type specific mouse mesoconnectome using gene expression data Open
Reconstructing brain connectivity at sufficient resolution for computational models designed to study the biophysical mechanisms underlying cognitive processes is extremely challenging. For such a purpose, a mesoconnectome that includes la…
View article: Scalable Brain Atlas Composer: web-based API for brain atlasing and visualization workflows
Scalable Brain Atlas Composer: web-based API for brain atlasing and visualization workflows Open
View article: SBA Composer: Web-based brain atlasing platform for multi-modal data integration
SBA Composer: Web-based brain atlasing platform for multi-modal data integration Open
View article: A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas
A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas Open
Cortical activity has distinct features across scales, from the spiking statistics of individual cells to global resting-state networks. We here describe the first full-density multi-area spiking network model of cortex, using macaque visu…
View article: FIIND: Ferret Interactive Integrated Neurodevelopment Atlas
FIIND: Ferret Interactive Integrated Neurodevelopment Atlas Open
The first days after birth in ferrets provide a privileged view of the development of a complex mammalian brain. Unlike mice, ferrets develop a rich pattern of deep neocortical folds and cortico- cortical connections. Unlike humans and oth…
View article: Scalable Brain Atlas Composer: web-based brain atlasing toolkit for integrative data exploration
Scalable Brain Atlas Composer: web-based brain atlasing toolkit for integrative data exploration Open
View article: Multi-scale account of the network structure of macaque visual cortex
Multi-scale account of the network structure of macaque visual cortex Open
Cortical network structure has been extensively characterized at the level of local circuits and in terms of long-range connectivity, but seldom in a manner that integrates both of these scales. Furthermore, while the connectivity of corte…
View article: Correction: The missing link: Predicting connectomes from noisy and partially observed tract tracing data
Correction: The missing link: Predicting connectomes from noisy and partially observed tract tracing data Open
[This corrects the article DOI: 10.1371/journal.pcbi.1005374.].
View article: The missing link: Predicting connectomes from noisy and partially observed tract tracing data
The missing link: Predicting connectomes from noisy and partially observed tract tracing data Open
Our understanding of the wiring map of the brain, known as the connectome, has increased greatly in the last decade, mostly due to technological advancements in neuroimaging techniques and improvements in computational tools to interpret t…
View article: Mapping complementary features of cross‐species structural connectivity to construct realistic “Virtual Brains”
Mapping complementary features of cross‐species structural connectivity to construct realistic “Virtual Brains” Open
Modern systems neuroscience increasingly leans on large‐scale multi‐lab neuroinformatics initiatives to provide necessary capacity for biologically realistic modeling of primate whole‐brain activity. Here, we present a framework to assembl…
View article: Getting neuron morphologies registered to a brain atlas
Getting neuron morphologies registered to a brain atlas Open
View article: The Missing Link: Predicting Connectomes from Noisy and Partially Observed Tract Tracing Data
The Missing Link: Predicting Connectomes from Noisy and Partially Observed Tract Tracing Data Open
Our understanding of the wiring map of the brain, known as the connectome , has increased greatly in the last decade, mostly due to technological advancements in neuroimaging techniques and improvements in computational tools to interpret …
View article: HBP neuron morphology viewer
HBP neuron morphology viewer Open
View article: Construction of a multi-scale spiking model of macaque visual cortex
Construction of a multi-scale spiking model of macaque visual cortex Open
Understanding the relationship between structure and dynamics of the mammalian cortex is a key challenge of neuroscience. So far, it has been tackled in two ways: by modeling neurons or small circuits in great detail, and through large-sca…
View article: Feeding the human brain model
Feeding the human brain model Open
View article: The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases and Related Content
The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases and Related Content Open