Staff Profiles

Nuno Maçarico da Costa, Ph.D.

Investigator, Associate

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 Interests

Research Interests 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.


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

Research Programs

  • Neural Coding

Selected Publications View Publications

A scalable and modular automated pipeline for stitching of large electron microscopy datasets

July 26, 2022

Mahalingam G, Torres R, Kapner D, Trautman ET, Fliss T, Seshamani S, Perlman E, Young R, Kinn S, Buchanan J, Takeno MM, Yin W, Bumbarger DJ, Gwinn RP, Nyhus J, Lein E, Smith SJ, Reid RC, Khairy KA, Saalfeld S, Collman F, Macarico da Costa N

Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity

March 17, 2022

Turner NL, Macrina T, Bae JA, Yang R, Wilson AM, Schneider-Mizell C, Lee K, Lu R, Wu J, Bodor AL, Bleckert AA, Brittain D, Froudarakis E, Dorkenwald S, Collman F, Kemnitz N, Ih D, Silversmith WM, Zung J, Zlateski A, Tartavull I, Yu SC, Popovych S, Mu S, Wong W, Jordan CS, Castro M, Buchanan J, Bumbarger DJ, Takeno M, Torres R, Mahalingam G, Elabbady L, Li Y, Cobos E, Zhou P, Suckow S, Becker L, Paninski L, Polleux F, Reimer J, Tolias AS, Reid RC, da Costa NM, Seung HS

Structure and function of axo-axonic inhibition

December 1, 2021

Schneider-Mizell CM, Bodor AL, Collman F, Brittain D, Bleckert A, Dorkenwald S, Turner NL, Macrina T, Lee K, Lu R, Wu J, Zhuang J, Nandi A, Hu B, Buchanan J, Takeno MM, Torres R, Mahalingam G, Bumbarger DJ, Li Y, Chartrand T, Kemnitz N, Silversmith WM, Ih D, Zung J, Zlateski A, Tartavull I, Popovych S, Wong W, Castro M, Jordan CS, Froudarakis E, Becker L, Suckow S, Reimer J, Tolias AS, Anastassiou CA, Seung HS, Reid RC, da Costa NM

A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy

Nature Communications
October 2, 2020

Yin W, Brittain D, Borseth J, Scott ME, Williams D, Perkins J, Own CS, Murfitt M, Torres RM, Kapner D, Mahalingam G, Bleckert A, Castelli D, Reid D, Lee WA, Graham BJ, Takeno M, Bumbarger DJ, Farrell C, Reid RC, da Costa NM

Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes

Scientific Reports
September 28, 2018

Shahbazi A, Kinnison J, Vescovi R, Du M, Hill R, Joesch M, Takeno M, Zeng H, da Costa NM, Grutzendler J, Kasthuri N, Scheirer WJ

Visual physiology of the Layer 4 cortical circuit in silico

PLoS Computational Biology
November 12, 2018

Arkhipov A, Gouwens NW, Billeh YN, Gratiy S, Iyer R, Wei Z, Xu Z, Berg J, Buice M, Cain N, da Costa N, de Vries S, Denman D, Durand S, Feng D, Jarsky T, Lecoq J, Lee B, Li L, Mihalas S, Ocker GK, Olsen SR, Reid RC, Soler-LLavina G, Sorensen SA, Wang Q, Waters J, Scanziani M, Koch C

Large-scale neuroanatomy using LASSO: Loop-based Automated Serial Sectioning Operation

October 23, 2018

Lee TJ, Kumar A, Balwani AH, Brittain D, Kinn S, Tovey CA, Dyer EL, da Costa NM, Reid RC, Forest CR, Bumbarger DJ

Pyramidal Cells Make Specific Connections onto Smooth (GABAergic) Neurons in Mouse Visual Cortex

PLoS Biology
August 19, 2014

Bopp R, da Costa NM, Kampa BM, Martin KAC, Roth MM

How thalamus connects to spiny stellate cells in the cat's visual cortex

Journal of Neuroscience
February 2011

da Costa NM, Martin KA

Embedding of cortical representations by the superficial patch system

Cerebral Cortex
October 2011

Muir DR, Da Costa NM, Girardin CC, Naaman S, Omer DB, Ruesch E, Grinvald A, Douglas RJ

The synaptic organization of the claustral projection to the cat's visual cortex

Journal of Neuroscience
September 2010

da Costa NM, Fürsinger D, Martin KA

Whose Cortical Column Would that Be?

Frontiers in Neuroanatomy
May 2010

da Costa NM, Martin KA