Carsen Stringer
Principal Investigator
Ashburn, Virginia, United States
Summary
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Rockstar🎓
Top SchoolCarsen Stringer is a Principal Investigator at HHMI Janelia with a decade of experience bridging computational neuroscience, large-scale neural data analysis, and software engineering. Trained in applied math, physics, and computational neuroscience (UCL PhD), he leads the Stringer lab developing tools and analyses to reveal how visual features drive mouse behavior. An active open-source contributor, he has materially improved widely used repositories such as Cellpose (GUI and 2D/3D mask tools) and Suite2p (nonrigid registration and parallelized preprocessing), bringing rigorous engineering to neuroimaging pipelines. Known for turning complex imaging challenges into practical, scalable software, he combines hands-on coding with hypothesis-driven science and a knack for user-focused interface improvements.
9 years of coding experience
4 years of employment as a software developer
BS, Applied Mathematics, Physics, BS, Applied Mathematics, Physics at University of PittsburghDoctor of Philosophy (PhD), Computational Neuroscience, Doctor of Philosophy (PhD), Computational Neuroscience at University College London, U. of London
Github Skills (12)
algorithm10
algorithms10
computer-vision10
pyqt10
parallel-computing10
front-end-development10
python10
image-processing10
machine-learning9
user-interface8
graphical-user-interface8
ui-design8
Programming languages (7)
Github contributions (5)
MouseLand/suite2p
Jul 2018 - Jan 2023
cell detection in calcium imaging recordings
Role in this project:
Back-end Developer & Machine Learning Engineer
Back-end Developer & Machine Learning EngineerContributions:7 releases, 3 reviews, 1065 commits in 4 years 7 months
Contributions summary:Carsen implemented nonrigid registration, likely for improving the alignment of calcium imaging recordings to a reference frame. The nonrigid registration appears to involve techniques like phase correlation to compute motion correction, and the user worked on implementing a parallel processing framework for faster processing. The user also modified the code to handle multi-channel image data and incorporate a pre-processing step.
data-analysisneuroscienceimagingcalcium-imagingsignal-processing
MouseLand/cellpose
Feb 2020 - Jan 2023
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
Role in this project:Software Engineer
Software EngineerContributions:19 releases, 476 commits, 136 PRs in 3 years
Contributions summary:Carsen primarily worked on adding and modifying code related to the GUI interface of the cellpose software, particularly around drawing and mask-related functionalities. They introduced features such as the ability to merge masks, incorporate 3D drawing capabilities, and add tooltips. They also addressed several bugs related to loading, displaying, and saving segmentation data. The user also appears to have been involved in testing and ensuring the correct display of the segmentation results, including in the 2D and 3D views, and introduced and implemented various functions to control those parameters from the GUI.
loophuman-in-the-loopcell-biologycell-segmentationcapabilities
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