News
New paper in eLife: The NeuroML ecosystem for standardized multi-scale modeling in neuroscience (Ankur Sinha, Padraig Gleeson, , Bóris Marin, Salvador Dura-Bernal, Sotirios Panagiotou, Sharon Crook, Matteo Cantarelli, Robert C Cannon, Andrew P Davison, Harsha Gurnani, Robin Angus Silver)
New paper in eLife: The NeuroML ecosystem for standardized multi-scale modeling in neuroscience (Ankur Sinha, Padraig Gleeson, , Bóris Marin, Salvador Dura-Bernal, Sotirios Panagiotou, Sharon Crook, Matteo Cantarelli, Robert C Cannon, Andrew P Davison, Harsha [...]
Half day hands-on NeuroML tutorial at CNS*2021 Online
A half day hands-on NeuroML tutorial was held at the 30th annual meeting of the Organization for Computational Neurosciences (OCNS): CNS*2021 Online on 2nd July. The goal of the tutorial was to teach users to: build, [...]
New paper in Nature Neuroscience: Cerebellar granule cell axons support high-dimensional representations (Frederic Lanore, N. Alex Cayco-Gajic, Harsha Gurnani, Diccon Coyle & R. Angus Silver)
New paper in Nature Neuroscience: Cerebellar granule cell axons support high-dimensional representations (Frederic Lanore, N. Alex Cayco-Gajic, Harsha Gurnani, Diccon Coyle & R. Angus Silver) In classical theories of cerebellar cortex, high-dimensional sensorimotor representations are used [...]
New paper in Biomedical Optics Express: Precompensation of 3D field distortions in remote focus two-photon microscopy (Antoine M. Valera, Fiona C. Neufeldt, Paul A. Kirkby, John E. Mitchell, and R. Angus Silver)
Remote focusing is widely used in 3D two-photon microscopy and 3D photostimulation because it enables fast axial scanning without moving the objective lens or specimen. However, due to the design constraints of microscope optics, remote [...]
New paper in Neuron: Multidimensional population activity in an electrically coupled inhibitory circuit in the cerebellar cortex (Gurnari, Silver)
Inhibitory neurons orchestrate the activity of excitatory neurons and play key roles in circuit function. Although individual interneurons have been studied extensively, little is known about their properties at the population level. Using random-access 3D [...]
OSA Biophotonics Congress: Optics in the Life Sciences 2021
Angus was invited to speak at the OSA Biophotonics Congress: Optics in the Life Sciences, 2021: In this OSA Congress, the latest advances in molecular probe development, life science imaging, novel and more powerful optical [...]
NeuroML hackathon at HARMONY 2021
3 online NeuroML hackathon sessions were held during the COMBINE: HARMONY 2021 meeting on 23-25th March. The general theme of the sessions was: learn to build, visualise, analyse and simulate your models using NeuroML. More [...]
Computational and Systems Neuroscience (Cosyne) 2021
Alessandro presented their work "Cerebellar-like structure improves feedback-learning in recurrent neural networks" at the Computational and Systems Neuroscience (Cosyne) meeting in 2021. More information on Cosyne 2021 can be found on its website.
Open Source Brain was presented at the 9th Neurodata Without Borders (NWB) user days workshop
Open Source Brain was presented at the 9th Neurodata Without Borders (NWB) user days workshop: The workshop will focus primarily on user training, including lessons for complete beginners to NWB and training in more [...]
Federation of European Neurosciences (FENS) Forum 2020
Along with other members of the Host Society Committee, Tommy helped organize the 2020 Federation of European Neurosciences (FENS) Forum, which was held virtually in Glasgow, Scotland. Tommy chaired the Young Investigator Training Program sub-committee, [...]
New paper in Nature Methods: Real-time 3D movement correction for two-photon imaging in behaving animals (Griffiths VA, Valera AM, Lau JY, Roš H, Younts TJ, Marin B, Baragli C, Coyle D, Evans GJ, Konstantinou G, Koimtzis T, Nadella KMNS, Punde SA, Kirkby PA, Bianco IH, and Silver RA)
Two-photon microscopy is widely used to investigate brain function across multiple spatial scales. However, measurements of neural activity are compromised by brain movement in behaving animals. Brain motion-induced artifacts are typically corrected using post hoc [...]
New paper in PLoS Computational Biology: The SONATA data format for efficient description of large-scale network models (Dai K, Hernando J, Billeh YN, Gratiy SL, Planas J, Davison AP, Dura-Bernal S, Gleeson P, Devresse A, Dichter BK, Gevaert M, King JG, Van Geit WAH, Povolotsky AV, Muller E, Courcol J-D, Arkhipov A)
Increasing availability of comprehensive experimental datasets and of high-performance computing resources are driving rapid growth in scale, complexity, and biological realism of computational models in neuroscience. To support construction and simulation, as well as sharing [...]
Tommy Younts organized and chaired the 2019 Gordon Research Seminar on Dendrites
Tommy Younts organized and chaired the 2019 Gordon Research Seminar on Dendrites, which was held in Ventura CA USA in March 2019. This unique forum, which precedes the parent Gordon Research Conference, brought together top [...]
New Review in Neuron: Re-evaluating Circuit Mechanisms Underlying Pattern Separation (Cayco-Gajic, Silver)
When animals interact with complex environments, their neural circuits must separate overlapping patterns of activity that represent sensory and motor information. Pattern separation is thought to be a key function of several brain regions, including [...]
D3D 2.0 Released
D3D version 2.0 is now available on Github. D3D is a Java-based 3D reaction-diffusion simulator that uses either an explicit finite-difference method similar to that described by Crank (1975) or a Monte Carlo algorithm for non-overlapping hard spheres [...]
New paper in Frontiers in Neuroinformatics – NeuroMatic: An Integrated Open-Source Software Toolkit for Acquisition, Analysis and Simulation of Electrophysiological Data (Rothman, Silver)
Acquisition, analysis and simulation of electrophysiological properties of the nervous system require multiple software packages. This makes it difficult to conserve experimental metadata and track the analysis performed. It also complicates certain experimental approaches such [...]