Publications related to NeuroMorph: A Software Toolset for 3D Analysis of Neurite Morphology and Connectivity

Related publications (31)

PLUMED Tutorials: A collaborative, community-driven learning ecosystem

Michele Ceriotti, Guillaume André Jean Fraux

In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several cha ...

AIP Publishing2025

Liberating Libraries through Automated Fuzz Driver Generation: Striking a Balance without Consumer Code

Zurab Tsinadze, Mathias Josef Payer, Flavio Toffalini, Nicolas Daniel Badoux

Fuzz testing a software library requires developers to write fuzz drivers, specialized programs exercising the library. Given a driver, fuzzers generate interesting inputs that trigger the library’s bugs. Writing fuzz drivers manually is a cumbersome proce ...

Association for Computing Machinery (ACM)2025

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets

Martin Weigert

Volume electron microscopy is the method of choice for the in situ interrogation of cellular ultrastructure at the nanometer scale, and with the increase in large raw image datasets generated, improving computational strategies for image segmentation and s ...

Nature Portfolio2024

Aggregating Spatial and Photometric Context for Photometric Stereo

David Honzátko

Photometric stereo, a computer vision technique for estimating the 3D shape of objects through images captured under varying illumination conditions, has been a topic of research for nearly four decades. In its general formulation, photometric stereo is an ...

EPFL2024

The multimodality cell segmentation challenge: toward universal solutions

Maxime Emmanuel Scheder, Jun Ma, Sahand Jamal Rahi, Xin Yang, Vojislav Gligorovski, Marco Labagnara

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in different experimen ...

Nature Publishing Group2024

Incorporating Projective Geometry into Deep Learning

Michal Jan Tyszkiewicz

In this thesis we explore the applications of projective geometry, a mathematical theory of the relation between 3D scenes and their 2D images, in modern learning-based computer vision systems. This is an interesting research question which contradicts the ...

EPFL2024

A bistable inhibitory optoGPCR for multiplexed optogenetic control of neural circuits

Mauro Pulin

Information is transmitted between brain regions through the release of neurotransmitters from long-range projecting axons. Understanding how the activity of such long-range connections contributes to behavior requires efficient methods for reversibly mani ...

Nature Publishing Group2024

Compact and effective photon-resolved image scanning microscope

Giorgio Tortarolo

Fluorescence confocal laser-scanning microscopy (LSM) is one of the most popular tools for life science research. This popularity is expected to grow thanks to single-photon array detectors tailored for LSM. These detectors offer unique single-photon spati ...

Spie-Soc Photo-Optical Instrumentation Engineers2024

Development and clinical validation of computational imaging biomarkers for neurodegenerative diseases

Veronica Lily Ravano

Neurodegenerative and neuroinflammatory disorders often involve complex pathophysiological mechanisms that are â to this date â only partially understood. A more comprehensive understanding of those microstructural processes and their characterization ...

EPFL2024

Creating Trust by Abolishing Hierarchies

Mathias Josef Payer, Edouard Bugnion, Evangelos Marios Kogias, Adrien Ghosn, Charly Nicolas Lucien Castes, Yuchen Qian, Neelu Shivprakash Kalani

Software is going through a trust crisis. Privileged code is no longer trusted and processes insufficiently protect user code from unverified libraries. While usually treated separately, confidential computing and program compartmentalization are both symp ...

Association for Computing Machinery2023

Robust Collaborative Learning with Linear Gradient Overhead

Rachid Guerraoui, Nirupam Gupta, Rafaël Benjamin Pinot, Le Nguyen Hoang, Sadegh Farhadkhani, John Stephan

Collaborative learning algorithms, such as distributed SGD (or D-SGD), are prone to faulty machines that may deviate from their prescribed algorithm because of software or hardware bugs, poisoned data or malicious behaviors. While many solutions have been ...

PLMR2023

Assemblies, synapse clustering and network topology interact with plasticity to explain structure-function relationships of the cortical connectome

Eilif Benjamin Muller, Michael Reimann, Marwan Muhammad Ahmed Abdellah, James Gonzalo King, András Ecker, Pramod Shivaji Kumbhar, Giuseppe Chindemi, Daniela Egas Santander, James Bryden Isbister, Ioannis Magkanaris, Sirio Bolaños Puchet, Jorge Blanco Alonso

Synaptic plasticity underlies the brain’s ability to learn and adapt. While experiments in brain slices have revealed mechanisms and protocols for the induction of plasticity between pairs of neurons, how these synaptic changes are coordinated in biologica ...

2024

Principles of Network Plasticity in Neocortical Microcircuits

András Ecker

Synaptic plasticity underlies our ability to learn and adapt to the constantly changing environment. The phenomenon of synapses changing their efficacy in an activity-dependent manner is often studied in small groups of neurons in vitro or indirectly throu ...

EPFL2023

Automated neuron tracking inside moving and deforming C. elegans using deep learning and targeted augmentation

Ariane Andrée Marie Delrocq, Sahand Jamal Rahi

Reading out neuronal activity from three-dimensional (3D) functional imaging requires segmenting and tracking individual neurons. This is challenging in behaving animals if the brain moves and deforms. The traditional approach is to train a convolutional n ...

Nature Publishing Group2023

lifex-ep: a robust and efficient software for cardiac electrophysiology simulations

Alfio Quarteroni, Francesco Regazzoni, Stefano Pagani

Background: Simulating the cardiac function requires the numerical solution of multi-physics and multi-scale mathematical models. This underscores the need for streamlined, accurate, and high-performance computational tools. Despite the dedicated endeavors ...

BMC2023

Machine-Learning-Enhanced Procedural Modeling for 4D Historical Cities Reconstruction

Frédéric Kaplan, Isabella Di Lenardo, Rémi Guillaume Petitpierre, Beatrice Vaienti

The generation of 3D models depicting cities in the past holds great potential for documentation and educational purposes. However, it is often hindered by incomplete historical data and the specialized expertise required. To address these challenges, we p ...

2023

Modeling and simulation of neocortical micro- and mesocircuitry. Part II: Physiology and experimentation

Weina Ji, Henry Markram, Felix Schürmann, Daniel Keller, Eilif Benjamin Muller, Michael Reimann, Werner Alfons Hilda Van Geit, Srikanth Ramaswamy, Matthias Wolf, James Gonzalo King, Alexis Arnaudon, András Ecker, Rajnish Ranjan, Jean-Denis Georges Emile Courcol, Armando Romani, Pramod Shivaji Kumbhar, Judit Planas Carbonell, Giuseppe Chindemi, Michael Emiel Gevaert, Christian Andreas Rössert, Fernando Joaquim Leite Pereira, Omar Awile, Mustafa Anil Tuncel, Daniela Egas Santander, James Bryden Isbister, Natali Barros Zulaica, Samuel Lieven D. Lapere, Sirio Bolaños Puchet, Maria Reva, Genrich Ivaska, Tanguy Pierre Louis Damart, Darshan Mandge, Joni Henrikki Herttuainen, Christoph Pokorny, Elvis Boci, Vishal Sood, Thomas Brice Delemontex, Aleksandra Zuzanna Teska, Polina Litvak, Alexander Dietz, Jorge Blanco Alonso, Gianluca Ficarelli

Cortical dynamics underlie many cognitive processes and emerge from complex multi-scale interactions, which are challenging to study in vivo. Large-scale, biophysically detailed models offer a tool which can complement laboratory approaches. We present a m ...

2024

Deep Learning for 3D Surface Modelling and Reconstruction

Benoît Alain René Guillard

In recent years, there has been a significant revolution in the field of deep learning, which has demonstrated its effectiveness in automatically capturing intricate patterns from large datasets. However, the majority of these successes in Computer Vision ...

EPFL2023

Multi-site, Multi-domain Airway Tree Modeling

Jiancheng Yang

Open international challenges are becoming the de facto standard for assessing computer vision and image analysis algorithms. In recent years, new methods have extended the reach of pulmonary airway segmentation that is closer to the limit of image resolut ...

Elsevier2023

3D reconstruction of curvilinear one-dimensional objects viewed in transmission electron microscopy

Gulnaz Ganeeva

To obtain a more complete understanding of material microstructure at the nanoscale and to gain profound insights into their properties, there is a growing need for more efficient and precise methods that can streamline the process of 3D imaging using a tr ...

EPFL2023