doi.bio/nicholas_james_sofroniew

Nicholas James Sofroniew

Early Life and Education

Nicholas James Sofroniew is a mathematician, scientist, and engineer. He obtained his Bachelor's Degree (2005-2008) and Master's Degree (2009) in Mathematics from the University of Cambridge, UK, specialising in Analysis and Combinatorics.

Career

Sofroniew is currently a Research Scientist in the lab of Karel Svoboda at the Janelia Research Campus in Ashburn, Virginia, USA. He completed his PhD in Neuroscience as part of a joint graduate program between the University of Cambridge and the Janelia Research Campus (2009-2013). From 2013 to 2016, he performed post-doctoral work at Janelia with Svoboda and Jeremy Freeman.

Sofroniew's research interests lie in reverse engineering the neurobiological basis of intelligence. He combines large-scale recordings of neuronal activity in behaving mice with detailed molecular profiling of the recorded neurons. His work requires expertise in biology, mathematics, and engineering, and he develops novel technologies as needed.

Publications and Online Presence

Sofroniew has a GitHub account with several public repositories, including:

• napari-training-course: Lectures for a napari training course
• electron-johnny-five-examples: Example electron apps using johnny-five to control hardware
• tutorial-scipy2021-bioimage-analysis-fundamentals: Tutorial for SciPy 2021 Bioimage Analysis Fundamentals in Python

He also has a Google Scholar profile with citations and co-authors listed.

Nicholas James Sofroniew

Overview

Nicholas James Sofroniew is a Research Scientist in the lab of Karel Svoboda at the Janelia Research Campus, Ashburn, Virginia, USA. His work focuses on reverse engineering the neurobiological basis of intelligence by combining large-scale recordings of neuronal activity with detailed molecular profiling. Sofroniew's academic and research background spans biology, mathematics, and engineering, and he develops novel technologies to achieve his research goals.

Education

• Bachelor's Degree in Mathematics (2005-2008), University of Cambridge, UK: Specialization in Analysis and Combinatorics.
• Master's Degree in Mathematics (2009), University of Cambridge, UK: Continuing his specialization in Analysis and Combinatorics.
• PhD in Neuroscience (2009-2013), Joint program between the University of Cambridge and the Janelia Research Campus: Sofroniew spent the first year of this program doing molecular neuroscience research with C. elegans in the lab of Howard Baylis at Cambridge, before transitioning to systems neuroscience research in Karel Svoboda's lab at Janelia.

Professional Experience

• Post-Doctoral Work (2013-2016), Janelia Research Campus: Sofroniew continued his research at Janelia with Karel Svoboda and Jeremy Freeman after completing his PhD.
• Postdoctoral Associate, Janelia Research Campus: Sofroniew's current position, where he probes cortical processing across multiple areas during complex navigation behavior.

Notable Works and Achievements

• Large field of view, high-resolution microscope (2017): Inventor on a patent for a microscope system that enables high-resolution imaging within a large volume, allowing for the study of activity across populations of neurons.
• Neural coding in barrel cortex during whisker-guided locomotion (eLife, 2015): This study explored neural coding in the barrel cortex of head-fixed mice navigating a tactile virtual reality environment, revealing the role of the barrel cortex in wall-tracking behavior.
• Mapping brain activity at scale with cluster computing (Nature Methods, 2014): Sofroniew and colleagues presented Thunder, a library of analytical tools built on Apache Spark for large-scale distributed computing, aiding in the analysis of large and complex neural data.
• Natural whisker-guided behavior by head-fixed mice in tactile virtual reality (Journal of Neuroscience, 2014): The paper describes a whisker-based tactile virtual reality system for head-fixed mice, allowing for the study of natural movements and precise control of sensorimotor variables during tactile navigation.
• Silver Medal at the 37th International Chemistry Olympiad in Taipei, Taiwan: Sofroniew was one of the top four high school students in Chemistry in the USA.

Affiliations

• Chan Zuckerberg Initiative: Sofroniew is affiliated with the Chan Zuckerberg Initiative, working on AI for Biology and Science.

- napari: Served on the steering council and contributed significantly to the code base of napari, a community-run open-source software project providing a multi-dimensional image viewer and analysis platform for Python.

Nicholas James Sofroniew

Early Life and Education

Nicholas James Sofroniew is a mathematician, scientist, and engineer. He obtained his Bachelor's Degree (2005-2008) and Master's Degree (2009) in Mathematics from the University of Cambridge, UK, specialising in Analysis and Combinatorics. During his time at Cambridge, Sofroniew also spent a year conducting molecular neuroscience research using C. elegans in the lab of Howard Baylis.

Career

Sofroniew currently works as a Research Scientist in the lab of Karel Svoboda at the Janelia Research Campus in Ashburn, Virginia. He completed his PhD in Neuroscience as part of a joint graduate program between the University of Cambridge and the Janelia Research Campus (2009-2013). From 2013 to 2016, he performed postdoctoral work at Janelia with Karel Svoboda and Jeremy Freeman.

Sofroniew's research interests lie in reverse engineering the neurobiological basis of intelligence. To achieve this, he combines large-scale recordings of neuronal activity in behaving mice with detailed molecular profiling of the recorded neurons. His work involves developing novel technologies and bridging the fields of biology, mathematics, and engineering.

Notable Works

Sofroniew has contributed to several notable projects and publications. Here are some of his most important works:

• Neural coding in barrel cortex during whisker-guided locomotion (2015): This study explored neural coding in the barrel cortex of head-fixed mice navigating through a tactile virtual reality environment.
• Natural whisker-guided behaviour by head-fixed mice in tactile virtual reality (2014): The project presented a whisker-based tactile virtual reality system for head-fixed mice, allowing for the precise control of sensorimotor variables during natural tactile navigation.
• Mapping brain activity at scale with cluster computing (2014): Sofroniew and his team introduced Thunder, a library of analytical tools built on the Apache Spark platform for large-scale distributed computing, to address the challenges of analysing large and complex neural data.
• Large field of view, high-resolution microscope (2017): This invention is a microscope system that enables high-resolution imaging within a large volume, facilitating the study of activity across populations of neurons.

Awards and Recognition

Sofroniew has received recognition for his work, including:

• Silver Medal at the 37th International Chemistry Olympiad in Taipei, Taiwan, where he represented Team USA as one of the top four high-school students in Chemistry.

Affiliations

• Chan Zuckerberg Initiative
• University of Cambridge
• Janelia Research Campus

Youtube Videos

Youtube Title: Nick Sofroniew — napari: a fast, interactive, multi-dimensional image viewer … — BIDS ImageXD 2021

Youtube Link: link

Youtube Channel Name: Berkeley Institute for Data Science (BIDS)

Youtube Channel Link: https://www.youtube.com/@UCBIDS

Nick Sofroniew — napari: a fast, interactive, multi-dimensional image viewer ... — BIDS ImageXD 2021

Youtube Title: Nicholas Sofroniew: "napari: a Python multi-dimensional image visualization and analysis…"

Youtube Link: link

Youtube Channel Name: Howard Hughes Medical Institute (HHMI)

Youtube Channel Link: https://www.youtube.com/@hhmi

Nicholas Sofroniew: "napari: a Python multi-dimensional image visualization and analysis..."

Youtube Title: Interactive Image Processing at Scale

Youtube Link: link

Youtube Channel Name: Coiled

Youtube Channel Link: https://www.youtube.com/@Coiled

Interactive Image Processing at Scale

Youtube Title: Multi-dimensional image visualization in Python using napari [NEUBIAS Academy@Home] webinar

Youtube Link: link

Youtube Channel Name: NEUBIAS

Youtube Channel Link: https://www.youtube.com/@NEUBIAS

!Multi-dimensional image visualization in Python using napari [NEUBIAS Academy@Home] webinar

Youtube Title: 1: Mesoscale two-photon calcium imaging with the 2p-RAM

Youtube Link: link

Youtube Channel Name: Nicholas Sofroniew

Youtube Channel Link: https://www.youtube.com/@nicholassofroniew7740

1: Mesoscale two-photon calcium imaging with the 2p-RAM

Youtube Title: I2K 2020 tutorial: Bioimage analysis fundamentals in Python with scikit-image, napari & friends

Youtube Link: link

Youtube Channel Name: Janelia Conferences, Workshops & Seminars

Youtube Channel Link: https://www.youtube.com/@janeliaconferencesworkshop3843

I2K 2020 tutorial: Bioimage analysis fundamentals in Python with scikit-image, napari & friends

Youtube Title: 'Virtual reality' for mice to aid neural research - BBC Click

Youtube Link: link

Youtube Channel Name: BBC Click

Youtube Channel Link: https://www.youtube.com/@BBCClick

'Virtual reality' for mice to aid neural research - BBC Click

Youtube Title: Soft matter and nanomaterials characterization by cryogenic transmission electron microscopy

Youtube Link: link

Youtube Channel Name: Materials Research Society

Youtube Channel Link: https://www.youtube.com/@MaterialsResearchSociety

Soft matter and nanomaterials characterization by cryogenic transmission electron microscopy

Youtube Title: Eyes of Science - Innovators

Youtube Link: link

Youtube Channel Name: National Science Foundation News

Youtube Channel Link: https://www.youtube.com/@NSFScience

Eyes of Science - Innovators

Youtube Title: Dr. Nicholas Bruns of Summit Eye Care

Youtube Link: link

Youtube Channel Name: Summit Eye Care

Youtube Channel Link: https://www.youtube.com/@summiteyecareofwisconsin

Dr. Nicholas Bruns of Summit Eye Care

Youtube Title: Scientists create tech to tackle dry eye disease

Youtube Link: link

Youtube Channel Name: AP Archive

Youtube Channel Link: https://www.youtube.com/@APArchive

Scientists create tech to tackle dry eye disease

Youtube Title: Quantum Frontiers Lecture: Don Eigler of IBM

Youtube Link: link

Youtube Channel Name: Institute for Quantum Computing

Youtube Channel Link: https://www.youtube.com/@QuantumIQC

Quantum Frontiers Lecture: Don Eigler of IBM

Youtube Title: FluoroSync™ Interface

Youtube Link: link

Youtube Channel Name: Boston Scientific: Chronic Pain and Spinal Cord Stimulation (SCS)

Youtube Channel Link: https://www.youtube.com/@bscineuro

FluoroSync™ Interface

Youtube Title: Scalable Research: Optometry and Vision Science

Youtube Link: link

Youtube Channel Name: UNSW Science

Youtube Channel Link: https://www.youtube.com/@UNSWScience

Scalable Research: Optometry and Vision Science

Youtube Title: Dr S Episode 1

Youtube Link: link

Youtube Channel Name: FluoreSCENE Media

Youtube Channel Link: https://www.youtube.com/@Fluorescene

Dr S Episode 1

Youtube Title: Dr. Carl Zorowski Memorial and Distinguished Lecture Series Seminar - Dr. Michael Sutton (9/10/2021)

Youtube Link: link

Youtube Channel Name: NC State MAE

Youtube Channel Link: https://www.youtube.com/@ncstatemae

Dr. Carl Zorowski Memorial and Distinguished Lecture Series Seminar - Dr. Michael Sutton (9/10/2021)

Youtube Title: Abstract Submissions 2018

Youtube Link: link

Youtube Channel Name: Society for Neuroscience

Youtube Channel Link: https://www.youtube.com/@sfnvideo

Abstract Submissions 2018

Youtube Title: Speciation II

Youtube Link: link

Youtube Channel Name: Simons Institute

Youtube Channel Link: https://www.youtube.com/@SimonsInstituteTOC

Speciation II

Youtube Videos

Youtube Title: Nick Sofroniew — napari: a fast, interactive, multi-dimensional image viewer … — BIDS ImageXD 2021

Youtube Link: link

Youtube Channel Name: Berkeley Institute for Data Science (BIDS)

Youtube Channel Link: https://www.youtube.com/@UCBIDS

Nick Sofroniew — napari: a fast, interactive, multi-dimensional image viewer ... — BIDS ImageXD 2021

Youtube Title: Nicholas Sofroniew: "napari: a Python multi-dimensional image visualization and analysis…"

Youtube Link: link

Youtube Channel Name: Howard Hughes Medical Institute (HHMI)

Youtube Channel Link: https://www.youtube.com/@hhmi

Nicholas Sofroniew: "napari: a Python multi-dimensional image visualization and analysis..."

Youtube Title: Interactive Image Processing at Scale

Youtube Link: link

Youtube Channel Name: Coiled

Youtube Channel Link: https://www.youtube.com/@Coiled

Interactive Image Processing at Scale

Youtube Title: Multi-dimensional image visualization in Python using napari [NEUBIAS Academy@Home] webinar

Youtube Link: link

Youtube Channel Name: NEUBIAS

Youtube Channel Link: https://www.youtube.com/@NEUBIAS

!Multi-dimensional image visualization in Python using napari [NEUBIAS Academy@Home] webinar

Youtube Title: 1: Mesoscale two-photon calcium imaging with the 2p-RAM

Youtube Link: link

Youtube Channel Name: Nicholas Sofroniew

Youtube Channel Link: https://www.youtube.com/@nicholassofroniew7740

1: Mesoscale two-photon calcium imaging with the 2p-RAM

Youtube Title: I2K 2020 tutorial: Bioimage analysis fundamentals in Python with scikit-image, napari & friends

Youtube Link: link

Youtube Channel Name: Janelia Conferences, Workshops & Seminars

Youtube Channel Link: https://www.youtube.com/@janeliaconferencesworkshop3843

I2K 2020 tutorial: Bioimage analysis fundamentals in Python with scikit-image, napari & friends

Youtube Title: 'Virtual reality' for mice to aid neural research - BBC Click

Youtube Link: link

Youtube Channel Name: BBC Click

Youtube Channel Link: https://www.youtube.com/@BBCClick

'Virtual reality' for mice to aid neural research - BBC Click

Youtube Title: Soft matter and nanomaterials characterization by cryogenic transmission electron microscopy

Youtube Link: link

Youtube Channel Name: Materials Research Society

Youtube Channel Link: https://www.youtube.com/@MaterialsResearchSociety

Soft matter and nanomaterials characterization by cryogenic transmission electron microscopy

Youtube Title: Eyes of Science - Innovators

Youtube Link: link

Youtube Channel Name: National Science Foundation News

Youtube Channel Link: https://www.youtube.com/@NSFScience

Eyes of Science - Innovators

Youtube Title: Dr. Nicholas Bruns of Summit Eye Care

Youtube Link: link

Youtube Channel Name: Summit Eye Care

Youtube Channel Link: https://www.youtube.com/@summiteyecareofwisconsin

Dr. Nicholas Bruns of Summit Eye Care

Youtube Title: Scientists create tech to tackle dry eye disease

Youtube Link: link

Youtube Channel Name: AP Archive

Youtube Channel Link: https://www.youtube.com/@APArchive

Scientists create tech to tackle dry eye disease

Youtube Title: Quantum Frontiers Lecture: Don Eigler of IBM

Youtube Link: link

Youtube Channel Name: Institute for Quantum Computing

Youtube Channel Link: https://www.youtube.com/@QuantumIQC

Quantum Frontiers Lecture: Don Eigler of IBM

Youtube Title: FluoroSync™ Interface

Youtube Link: link

Youtube Channel Name: Boston Scientific: Chronic Pain and Spinal Cord Stimulation (SCS)

Youtube Channel Link: https://www.youtube.com/@bscineuro

FluoroSync™ Interface

Youtube Title: Scalable Research: Optometry and Vision Science

Youtube Link: link

Youtube Channel Name: UNSW Science

Youtube Channel Link: https://www.youtube.com/@UNSWScience

Scalable Research: Optometry and Vision Science

Youtube Title: Dr S Episode 1

Youtube Link: link

Youtube Channel Name: FluoreSCENE Media

Youtube Channel Link: https://www.youtube.com/@Fluorescene

Dr S Episode 1

Youtube Title: Dr. Carl Zorowski Memorial and Distinguished Lecture Series Seminar - Dr. Michael Sutton (9/10/2021)

Youtube Link: link

Youtube Channel Name: NC State MAE

Youtube Channel Link: https://www.youtube.com/@ncstatemae

Dr. Carl Zorowski Memorial and Distinguished Lecture Series Seminar - Dr. Michael Sutton (9/10/2021)

Youtube Title: Abstract Submissions 2018

Youtube Link: link

Youtube Channel Name: Society for Neuroscience

Youtube Channel Link: https://www.youtube.com/@sfnvideo

Abstract Submissions 2018

Youtube Title: Speciation II

Youtube Link: link

Youtube Channel Name: Simons Institute

Youtube Channel Link: https://www.youtube.com/@SimonsInstituteTOC

Speciation II