Publications

Complete list of scientific contributions.

Featured Publications

Spatial Continuity of Neurons Explains Non-random Network Architecture

Reimann M. W., Santander D. E., Kanari L. & Barros-Zulaica N.

iScience · 2026

Temporal Topology Provides an Interpretable Framework for Neuronal Morphogenesis

Rigaux K., Castro A. F. & Kanari L.

Neuroinformatics · 2026

Generating Brain-wide Connectome Using Synthetic Axonal Morphologies

Petkantchin R., Berchet A., Peng H., Markram H. & Kanari L.

Nature Communications · 2025

Of Mice and Men: Dendritic Architecture Differentiates Human from Mouse Neuronal Networks

Kanari L., Shi Y., Arnaudon A., Barros-Zulaica N., Benavides-Piccione R., Coggan J. S., DeFelipe J., Hess K., Mansvelder H. D., Mertens E. J. et al.

iScience · 2025

Patents

Intellectual property arising from research on computational neuronal morphology.

Synthesis of Branching Morphologies

Lida Kanari · Kathryn Hess Bellwald · Henry Markram

Patent application

20190100470 ↗

Published

Peer-reviewed publications organised chronologically.

2026

A Multimodal Spatial Atlas of Transcriptomic, Morphological, and Electrophysiological Cell Type Densities in the Mouse Brain

Verasztó C., Roussel Y., Kanari L., Piluso S., Markram H. & Keller D.

PLOS Computational Biology · 22 · 2026

Spatial Continuity of Neurons Explains Non-random Network Architecture

Reimann M. W., Santander D. E., Kanari L. & Barros-Zulaica N.

iScience · 29 · 2026

Temporal Topology Provides an Interpretable Framework for Neuronal Morphogenesis

Rigaux K., Castro A. F. & Kanari L.

Neuroinformatics · 24 · 2026

2025

Breakdown and Repair of Metabolism in the Aging Brain

Shichkova P., Coggan J. S., Kanari L., Boci E., Favreau C., Antonel S. M., Keller D. & Markram H.

Frontiers in Science · 3 · 2025

Computational Generation of Long-range Axonal Morphologies

Berchet A., Petkantchin R., Markram H. & Kanari L.

Neuroinformatics · 23 · 2025

Generating Brain-wide Connectome Using Synthetic Axonal Morphologies

Petkantchin R., Berchet A., Peng H., Markram H. & Kanari L.

Nature Communications · 16 · 2025

Of Mice and Men: Dendritic Architecture Differentiates Human from Mouse Neuronal Networks

Kanari L., Shi Y., Arnaudon A., Barros-Zulaica N., Benavides-Piccione R., Coggan J. S., DeFelipe J., Hess K., Mansvelder H. D., Mertens E. J. et al.

iScience · 28 · 2025

2024

BlueCelluLab: Biologically Detailed Neural Network Experimentation API

Tuncel A., Van Geit W., Gevaert M., Torben-Nielsen B., Mandge D., Kılıç İ., Jaquier A., Muller E., Kanari L. & Markram H.

Journal of Open Source Software · 9 · 2024

Community-based Reconstruction and Simulation of a Full-scale Model of the Rat Hippocampus CA1 Region

Romani A., Antonietti A., Bella D., Budd J., Giacalone E., Kurban K., Sáray S., Abdellah M., Arnaudon A., Boci E. et al.

PLOS Biology · 22 · 2024

From Trees to Barcodes and Back Again II: Combinatorial and Probabilistic Aspects of a Topological Inverse Problem

Curry J., DeSha J., Garin A., Hess K., Kanari L. & Mallery B.

Computational Geometry · 116 · 2024

Modeling and Simulation of Neocortical Micro- and Mesocircuitry (Part I, Anatomy)

Reimann M. W., Bolaños-Puchet S., Courcol J., Egas Santander D., Arnaudon A., Coste B., Delalondre F., Delemontex T., Devresse A., Dictus H. et al.

eLife · 13 · 2024

2023

Controlling Morpho-electrophysiological Variability of Neurons with Detailed Biophysical Models

Arnaudon A., Reva M., Zbili M., Markram H., Van Geit W. & Kanari L.

iScience · 26 · 2023

Strong and Reliable Synaptic Communication Between Pyramidal Neurons in Adult Human Cerebral Cortex

Hunt S., Leibner Y., Mertens E. J., Barros-Zulaica N., Kanari L., Heistek T. S., Karnani M. M., Aardse R., Wilbers R., Heyer D. B. et al.

Cerebral Cortex · 33 · 2023

2022

A Tool for Mapping Microglial Morphology, morphOMICs, Reveals Brain-region and Sex-dependent Phenotypes

Colombo G., Cubero R. J. A., Kanari L., Venturino A., Schulz R., Scolamiero M., Agerberg J., Mathys H., Tsai L., Chachólski W. et al.

Nature Neuroscience · 25 · 2022

Computational Synthesis of Cortical Dendritic Morphologies

Kanari L., Dictus H., Chalimourda A., Arnaudon A., Van Geit W., Coste B., Shillcock J., Hess K. & Markram H.

Cell Reports · 39 · 2022

2021

Digital Reconstruction of the Neuro-Glia-Vascular Architecture

Zisis E., Keller D., Kanari L., Arnaudon A., Gevaert M., Delemontex T., Coste B., Foni A., Abdellah M., Calì C. et al.

Cerebral Cortex · 31 · 2021

2020

From Trees to Barcodes and Back Again: Theoretical and Statistical Perspectives

Kanari L., Garin A. & Hess K.

Algorithms · 13 · 2020

2019

Objective Morphological Classification of Neocortical Pyramidal Cells

Kanari L., Ramaswamy S., Shi Y., Morand S., Meystre J., Perin R., Abdellah M., Wang Y., Hess K. & Markram H.

Cerebral Cortex · 29 · 2019

2018

A Topological Representation of Branching Neuronal Morphologies

Kanari L., Dłotko P., Scolamiero M., Levi R., Shillcock J., Hess K. & Markram H.

Neuroinformatics · 16 · 2018

2017

Comprehensive Morpho-Electrotonic Analysis Shows 2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex

Deitcher Y., Eyal G., Kanari L., Verhoog M. B., Atenekeng Kahou G. A., Mansvelder H. D., De Kock C. P. & Segev I.

Cerebral Cortex · 27 · 2017

2016

Framework for Efficient Synthesis of Spatially Embedded Morphologies

Vanherpe L., Kanari L., Atenekeng G., Palacios J. & Shillcock J.

Physical Review E · 94 · 2016

In Situ Synthesis and Simulation of Polydisperse Amphiphilic Membranes

Vanherpe L., Kanari L., Atenekeng G., Palacios J. & Shillcock J.

International Journal of Advances in Engineering Sciences and Applied Mathematics · 8 · 2016

2015

Reconstruction and Simulation of Neocortical Microcircuitry

Markram H., Muller E., Ramaswamy S., Reimann M. W., Abdellah M., Sanchez C. A., Ailamaki A., Alonso-Nanclares L., Antille N., Arsever S. et al.

Cell · 163 · 2015

The Neocortical Microcircuit Collaboration Portal: A Resource for Rat Somatosensory Cortex

Ramaswamy S., Courcol J., Abdellah M., Adaszewski S. R., Antille N., Arsever S., Atenekeng G., Bilgili A., Brukau Y., Chalimourda A. et al.

Frontiers in Neural Circuits · 9 · 2015

Preprints

Current manuscripts available as preprints.

2026

A Detailed Model for Understanding the Human Neocortex

Barros-Zulaica N., Kanari L., Sood V., Rai P., Arnaudon A., Shi Y., Mandge D., Van Geit W., Zbili M., Reva M. et al.

bioRxiv · 2026

Chromatic Topological Mapping Reveals Organelle-specific Spatial Organization within Microglia

Agerberg J., Kanari L., Maes M. E., Chachólski W., Siegert S. & Scolamiero M.

bioRxiv · 2026

Contextual Cellular Growth (ConCeG) of Neural Cells for Realistic Grey Matter Tissue Generation for Diffusion MRI Simulations

Aird-Rossiter C., Şimşek K., Jallais M., Jones D. K., Kanari L. & Palombo M.

arXiv · 2026

Self-organized Tiling Generates Tissue-scale Hyperuniformity During Development

Siegert S., Kanari L. & Uçar M. C.

bioRxiv · 2026

Uncovering the Basis of Human Connectome Complexity: The Role of Neuronal Morphology

Barros-Zulaica N., Egas Santander D., Kanari L., Shi Y., Perin R., Pezzoli M., Benavides-Piccione R., DeFelipe J., de Kock C. P., Segev I. et al.

bioRxiv · 2026

2024

Deep Learning for Classifying Neuronal Morphologies: Combining Topological Data Analysis and Graph Neural Networks

Kanari L., Schmidt S., Casalegno F., Delattre É., Banjac J., Negrello T., Shi Y., Meystre J., Defferrard M., Schürmann F. et al.

bioRxiv · 2024