About
The NeuroRSE group at Flatiron Institute Center for Computational Neuroscience builds and maintains open source software for computational and systems neuroscience. We intend to create solid packages that can be relied and built upon, rather than chasing cutting-edge research.
What does RSE mean? A “research software engineer”, which is defined by the US-RSE professional organization as someone “who regularly use expertise in programming to advance research”.
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Our Projects
All of our projects are open-source python packages. We are always happy to get external contributors and happy to help new users get started!
CaImAn
CaImAn provides a full pipeline for analyzing single-cell optical physiology data – both calcium and voltage imaging data. Given raw data, CaImAn provides algorithms for motion-correction and the extraction of the locations of neural components and their corresponding calcium/voltage traces. It also includes extensive tools for visualizing data, results, and quality control.
nemos
A statistical modeling framework for systems neuroscience. Nemos, our latest software package, specializes in GPU-accelerated optimizations. Its current core functionality includes the implementation of the Generalized Linear Model (GLM) for spike train analysis.
plenoptic
plenoptic is a python library for model-based synthesis of perceptual stimuli. The generated stimuli enable interpretation of model properties through examination of features that are enhanced, suppressed, or descarded. More importantly, they can facilitate the scientific proceess, through use in perceptual or neural experiments aimed at validating/falsifying model predictions.
pynapple
pynapple is a light-weight python library for neurophysiological data analysis. The goal is to offer a versatile set of tools to study typical data in the field, i.e. time series (spike times, behavioral events, etc.) and time intervals (trials, brain states, etc.). It also provides users with generic functions for neuroscience such as tuning curves and cross-correlograms.
CCN Template
The CCN Template repo is not an actual python package, but an attempt to make and document all the many decisions that go into writing open-source python packages: structure, packaging, documentation, testing, etc. This is largely intended for our use, but hope it can serve as a resource for the broader community!
Members
Edoardo Balzani
Edoardo is the one of the principal developers of Nemos, a package for statistical modeling of neural activity. He earned his Ph.D. in Neuroscience from the Italian Institute of Technology in Genova, under the guidance of Valter Tucci. Before joining the Flatiron institute as a data scientist, he worked as a postdoc in Cristina Savin’s lab at NYU’s Center for Neural Science where he developed statistical methods for the analysis of neural spike trains during naturalistic behavior.
Billy Broderick
Billy Broderick received his Ph.D. from NYU’s Center for Neural Science, where he was advised by Eero Simoncelli and Jon Winawer. During his Ph.D., he studied how vision changes across the visual field using fMRI, psychophysics, and computational models. Before that, he worked as a research assistant at Duke University, spent a year at South China Normal University in Guangzhou, China as a Luce Scholar, and got his B.A. in neuroscience and mathematics at Oberlin College
Eric Thomson
Eric helps maintain CaImAn, the calcium imaging analysis platform. His main goal is to build software that works well and is accessible to experimentalists. He received his PhD in neuroscience from UCSD before working as a postdoc at Duke University with Miguel Nicolelis on sensory prosthetic systems. He then worked in computational optics with Roarke Horstmeyer and Eva Naumann, helping to develop a multi-camera microscope system. Before coming to Flatiron, Eric was a data scientist at NIH/NIEHS, working with multiple neuroscience labs to analyze calcium imaging and electrophysiology data.
Guillaume Viejo
Guillaume Viejo joined the Center for Computational Neuroscience as a data scientist, where he focuses on developing software for analyzing neurophysiological data. He holds a Ph.D. in computational neuroscience from the Institute of Intelligent Systems and Robotics at the Pierre and Marie Curie University in Paris, France. After completing his doctorate, Guillaume worked as a postdoctoral fellow at the Montreal Neurological Institute, where he studied the head-direction system (also known as the brain’s compass) in rodents.