Nuno Maçarico da Costa

Cell-type-specific parallel pathways in the canonical cortical microcircuit

The paper maps connectivity in mouse primary visual cortex, revealing cell-type-specific parallel pathways for top-down and bottom-up processing.

A quantitative census of millions of postsynaptic structures in a large electron microscopy volume of mouse visual cortex

The paper presents a computational pipeline for classifying postsynaptic targets in neuronal meshes, achieving high accuracy on mouse visual cortex data and demonstrating generalizability to other connectomes.

Hebb's Vision: The Structural Underpinnings of Hebbian Assemblies

The paper identifies neural assemblies consistent with Hebb's theory using a novel dataset linking optical physiology to connectivity, finding they are structurally integrated but not defined by strong monosynaptic connections.

CAVE: Connectome Annotation Versioning Engine

CAVE enables reproducible connectome analysis in large-scale datasets during ongoing annotation and proofreading.

NEURD offers automated proofreading and feature extraction for connectomics

NEURD automates proofreading and feature extraction from connectomics data to improve accuracy and accessibility of neural morphology analyses.

Functional connectomics spanning multiple areas of mouse visual cortex

The paper presents a functional connectomics dataset of mouse visual cortex, combining calcium imaging with EM reconstruction to study neural circuits and their connectivity.

Functional connectomics reveals general wiring rule in mouse visual cortex

Functionally similar neurons in mouse visual cortex connect preferentially across layers and areas, including feedback, and feature tuning, not receptive-field position, predicts synapses beyond axon-dendrite proximity.

An unsupervised map of excitatory neurons' dendritic morphology in the mouse visual cortex

The paper uses graph-based machine learning to analyze dendritic morphology of excitatory neurons in mouse visual cortex, finding a continuous morphological landscape rather than discrete types.

Multi-Layered Maps of Neuropil with Segmentation-Guided Contrastive Learning

SegCLR, a self-supervised learning method, enables classification of cellular subcompartments and cell types from 3D electron microscopy data with minimal labeled data.

The Synaptic Architecture of Layer 5 Thick Tufted Excitatory Neurons in the Visual Cortex of Mice

The paper investigates the synaptic connectivity of thick tufted layer 5 pyramidal neurons in the mouse visual cortex, revealing their local inhibitory and long-range excitatory connections.

Integrating EM and Patch-seq data: Synaptic connectivity and target specificity of predicted Sst transcriptomic types

The paper predicts MET-type identities from EM data and shows they have distinct connectivity patterns and synapse targets.

Foundation model of neural activity predicts response to new stimulus types and anatomy

This paper trains a foundation model on neural activity data to predict responses to new stimuli and anatomical features, showing strong generalization across mice and tasks.

Cell-type-specific inhibitory circuitry from a connectomic census of mouse visual cortex

Electron microscopy of 1352 neurons in a mouse visual cortex column reveals widespread cell-type-specific inhibition, a basket-cell-targeting disinhibitory class, and interneuron motif groups sharing excitatory targets.

Binary and analog variation of synapses between cortical pyramidal neurons

The paper maps synaptic connectivity between cortical pyramidal neurons and shows synapse size is modeled by a combination of binary and analog variables.

A Scalable and Modular Automated Pipeline for Stitching of Large Electron Microscopy Datasets

The paper presents a scalable pipeline for assembling large electron microscopy datasets into 3D volumes, achieving high throughput and modular design for efficient processing.

Perisomatic Features Enable Efficient and Dataset Wide Cell-Type Classifications Across Large-Scale Electron Microscopy Volumes

The paper uses electron microscopy data to classify cell types in the neocortex based on perisomatic features, showing that these features are sufficient for accurate classification even in large datasets.

Petascale neural circuit reconstruction: automated methods

Cloud-run convolutional nets aligned 19,939 serial EM sections of mouse visual cortex despite cracks and folds, segmented neurons and detected 523 million synapses; code and the reconstruction are public.

Oligodendrocyte precursor cells prune axons in the mouse neocortex

The paper identifies oligodendrocyte precursor cells (OPCs) as major contributors to axon pruning in the mouse neocortex through phagocytic activity.

Multiscale and multimodal reconstruction of cortical structure and function

The paper presents a semi-automated reconstruction of mouse primary visual cortex from electron microscopy data, revealing structural and functional relationships in cortical circuits.

A Petascale Automated Imaging Pipeline for Mapping Neuronal Circuits with High-throughput Transmission Electron Microscopy

The paper describes a high-throughput transmission electron microscopy pipeline for imaging neuronal circuits, achieving petascale data acquisition of mouse neocortex.

Chandelier cell anatomy and function reveal a variably distributed but common signal

The paper maps chandelier cell synapses onto pyramidal neurons and finds variability in synaptic input correlated with target neuron features, while showing functional correlation with arousal state.

EASE: EM-Assisted Source Extraction from calcium imaging data

The paper introduces EASE, a method that matches calcium imaging signals to EM-derived cell segments in mouse visual cortex, enabling dendritic functional analysis and denoising.

Visual physiology of the Layer 4 cortical circuit in silico

The paper develops a biophysically detailed in silico model of layer 4 of the mouse primary visual cortex, showing how functional synaptic connectivity reproduces experimental observations of neuronal responses to visual stimuli.

Flexible Learning-Free Segmentation and Reconstruction for Sparse Neuronal Circuit Tracing

This paper introduces a fast, learning-free method for sparse segmentation and reconstruction of neural volumes, demonstrating high-quality results across multiple imaging modalities.

A suite of transgenic driver and reporter mouse lines with enhanced brain cell type targeting and functionality

The paper introduces a new set of transgenic mouse lines for precise targeting and manipulation of brain cell types, enhancing genetic tools for neuroscience research.

A weighted graph of the projections to mouse auditory cortex

The paper constructs a weighted graph of input sources to the mouse primary auditory cortex, revealing the proportion and hierarchy of cortical and subcortical projections.

Fast Assembling of Neuron Fragments in Serial 3D Sections

NeuronStitcher is a software suite that stitches non-overlapping neuron fragments from 3D image sections to reconstruct large and complex neurons efficiently.