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people

Nuno Maçarico da Costa

Investigator

teams /
Allenite

Nuno Maçarico da Costa joined the Allen Institute in 2013 as an Assistant Investigator in the Neural Coding department. He leads the Network Anatomy group in its efforts map the wiring diagram of the mouse neocortex and its functional connectivity. Nuno graduated in Biology from the Faculty of Science of the University of Lisbon. Afterwards he moved north to Copenhagen, Denmark, where he studied the interactions between the hippocampus and prefrontal cortex in rats. After this period with the charming Danes, Nuno returned to Portugal and joined the Doctoral Program in Biology and Medicine of the Gulbenkian Foundation. He performed his doctoral research in the Institute of Neuroinformatics in Zurich and obtained a PhD degree in Natural Sciences from the Swiss Federal Institute of Technology. During his PhD he described the fine structural detail of the thalamocortical pathway to cat visual cortex using light and electron correlated microscopy. He stayed in Zurich as a post-doc fellow and later as a Junior Group Leader investigating the network anatomy of the neocortex in several mammalian species.

research focus

Every thought, every idea, every memory, every decision, and every action we make, arises from the activity of neurons in our brains. Of all brain structures, the neocortex, is arguably the most critical structure that makes us human, however “Our ignorance is such that, even today, to a question so important and yet so simple as the general connections of nerve cells, science does not have an answer for the more or less probable hypotheses”(Ramon y Cajal, 1891). My current research focus on describing the wiring diagram of the mouse primary visual cortex and investigating the computations implemented by its architecture. I am interested in how conserved is the architecture over different cortical areas and species, how general are its operations and how these operations finally translate to behavior. To answer these questions we are using state of the art light and electron microscopy techniques combined with the power of genetics of the mouse animal model.

Expertise

  • Neuroanatomy
  • in vivo electrophysiology
  • Light and electron correlated microscopy

Research Programs

  • Neural Coding

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Scientists complete largest wiring diagram and functional map of the brain to date
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Revealing the largest wiring diagram and functional map of the brain through MICrONS
Scientists have created the largest wiring diagram and functional map of an animal brain
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Attempting the impossible: A 20-year journey to learn the language of the brain
In what is considered the most complicated neuroscience experiment ever attempted, scientists from the Allen Institute and global collaborators have...

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featured publications

publication / 2025
The synaptic architecture of layer 5 thick tufted excitatory neurons in mouse visual cortex
Nature Neuroscience
publication / 2025
An unsupervised map of excitatory neuron dendritic morphology in the mouse visual cortex
Nature Communications
publication / 2025
CAVE: Connectome Annotation Versioning Engine
Nature Methods
publication / 2025
NEURD offers automated proofreading and feature extraction for connectomics
Nature
publication / 2025
Inhibitory specificity from a connectomic census of mouse visual cortex
Nature
publication / 2025
Functional connectomics reveals general wiring rule in mouse visual cortex
Nature
publication / 2025
Perisomatic ultrastructure efficiently classifies cells in mouse cortex
Nature
publication / 2025
Foundation model of neural activity predicts response to new stimulus types
Nature
publication / 2024
Ultrastructural differences impact cilia shape and external exposure across cell classes in the visual cortex
Current biology: CB
publication / 2023
Multi-layered maps of neuropil with segmentation-guided contrastive learning
Nature Methods
publication / 2023
Emerging roles of oligodendrocyte precursor cells in neural circuit development and remodeling
Trends in Neurosciences
publication / 2022
Oligodendrocyte precursor cells ingest axons in the mouse neocortex
Proceedings of the National Academy of Sciences of the United States of America
publication / 2022
Binary and analog variation of synapses between cortical pyramidal neurons
eLife
publication / 2022
A scalable and modular automated pipeline for stitching of large electron microscopy datasets
eLife
publication / 2022
Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity
Cell
publication / 2021
Structure and function of axo-axonic inhibition
eLife
publication / 2020
A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy
Nature Communications
publication / 2018
Publisher Correction: Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes
Scientific Reports
publication / 2018
Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes
Scientific Reports
publication / 2017
Fast assembling of neuron fragments in serial 3D sections
Brain Informatics
publication
Connectomics of predicted Sst transcriptomic types in mouse visual cortex
Nature
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