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Research


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Research


Welcome! We are a research team at the Rowland Institute at Harvard University led by Mackenzie Mathis, PhD. In 2020 we are joining the Brain Mind Institute & Center for Neuroprosthetics at the Swiss Federal Institute of Technology, Lausanne.

The goal of the laboratory is to reverse engineer the neural circuits that drive adaptive motor behavior. We hope that by understanding the neural basis of adaptive motor control we can open new avenues in therapeutic research for neurological disease, help build better machine learning tools, and crucially, provide fundamental insights into brain function.  

Here are questions that guide us:

  • How do animals adapt to their environment over short and long timescales?

  • What neural computations enable adaptive behavior?

  • Can we make more biologically-inspired artificial intelligence by studying natural intelligence?

  • Can we use these circuit-level and machine-learning advances to restore function in neurodegeneration and neurological injury?

photo by Cassandra Klos for  Bloomberg Businessweek
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We believe behavior is an essential component to understanding neural function. As part of our quest to better understand behavior, we develop new tools to study more complex and natural movements. Here is some technology that we utilize, and develop, to answer those questions:

We develop computer vision tools, like DeepLabCut, to perform markerless pose estimation and behavioral analysis from any species in a multitude of settings. For our purposes, we use these key-points to study kinematics and motor learning during a variety of skills tasks, and during freely moving natural behaviors. We also will continue to collaborate with the Mathis Group on these types of tools.

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We also have developed a set of skilled motor tasks where mice can learn from a dynamically changing sensory landscape.

By combining concepts from machine learning and optimal motor control with the power of the mouse's genetics and accessibility, our lab aims to uncover fundamental principles that guide motor adaptation, learning, and motor control.

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We are using the latest techniques in 2-photon and deep brain imaging (including utilizing multi-area imaging with a 2-photon mesoscope), to uncover the neural correlates of adaptive behavior. We use optogenetics and chemogenetics to test what roles diverse areas have during behavior. Furthermore, we develop new computational models and tools to generate testable hypotheses and analyze our data.

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People


People


People

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Mackenzie Mathis, PhD
Principal Investigator, Rowland Fellow

mathis@rowland.harvard.edu
Office Location: 3rd Floor, 308
Google Scholar page | CV |More Info

 

Postdoctoral Fellows, Masters, & PhD Students

Gary Kane, PhD   Postdoctoral Fellow  gkane@rowland.harvard.edu, Office Location: 3rd Floor, 309  Google Scholar   Gary completed his PhD at Princeton, working on neural circuits of decision-making in rats. He joined the lab in July of 2018.

Gary Kane, PhD
Postdoctoral Fellow

gkane@rowland.harvard.edu, Office Location: 3rd Floor, 309
Google Scholar

Gary completed his PhD at Princeton, working on neural circuits of decision-making in rats. He joined the lab in July of 2018.

Kai Sandbrink   Masters student  sandbrink@rowland.harvard.edu, Office Location: 3rd Floor, 309  Kai is completing his masters thesis from ETH in the lab. He joined in March of 2019.

Kai Sandbrink
Masters student

sandbrink@rowland.harvard.edu, Office Location: 3rd Floor, 309

Kai is completing his masters thesis from ETH in the lab. He joined in March of 2019.

Max Günthner  PhD Student with the Bethge & Mathis Lab  Info coming soon! Welcome Max!!!

Max Günthner
PhD Student with the Bethge & Mathis Lab

Info coming soon! Welcome Max!!!

Undergraduate Researchers

Tom Biasi  Undergraduate student  He is a sophomore at Harvard studying computer science. He joined the lab in March of 2019.  He works on new neural networks for animal pose estimation.

Tom Biasi
Undergraduate student

He is a sophomore at Harvard studying computer science. He joined the lab in March of 2019.

He works on new neural networks for animal pose estimation.

Michael Beauzile   Undergraduate student  He is a junior pre-MD/PhD at Boston University studying Biomedical and Electrical Engineering. His interests include psychology, neuroanatomy and nanotechnology. He joined the lab in March of 2019.  He works on developing new motor adaptation behaviors & analysis tools

Michael Beauzile
Undergraduate student

He is a junior pre-MD/PhD at Boston University studying Biomedical and Electrical Engineering. His interests include psychology, neuroanatomy and nanotechnology. He joined the lab in March of 2019.

He works on developing new motor adaptation behaviors & analysis tools

Daniel Soberanes  Undergraduate Student  Daniel is a senior at Harvard studying Biomedical Engineering, with a focus on computer science and neuroengineering. His primary interest is brain-computer interfaces. He joined the lab in Sept. 2019.

Daniel Soberanes
Undergraduate Student

Daniel is a senior at Harvard studying Biomedical Engineering, with a focus on computer science and neuroengineering. His primary interest is brain-computer interfaces. He joined the lab in Sept. 2019.


Collaborators:

Alexander Mathis, PhD | https://www.mathislab.org/
Alexander collaborates closely with us on computational models of motor adaptation and learning, and using deep learning to quantify animal behavior (see DeepLabCut). His group is starting at EPFL in 2020!

Matthias Bethge, PhD | Bethgelab.org
Matthias and his group collaborate with us on using deep learning tools for pose estimation, neural data analysis, and predictive modeling.

Travis DeWolf, PhD | Applied Brain Research - Publications & Blog
Travis works with us on multi-area brain models


Alumni:

Tanmay Nath, PhD
postdoctoral fellow 2018-2019 | nath@rowland.harvard.ed; Tanmay completed his PhD focused on developing machine learning tools for biological systems. Tanmay worked with us on DeepLabCut 2.x (see Nath et al, 2019)! He is now a research scientist at Johns Hopkins University.

Eric Hepler
Animal Technician 2017-2019 | He worked with us on maintaining our precious mouse colony!

Adrian Hoffmann
Masters student 2018 | University of Tübingen, Neural Information Processing.
hoffmann@rowland.harvard.edu; Adrian completed his master's thesis in the lab through the University of Tübingen in 2018. He received a BS in Physics from Heidelberg University. Adrian is now a PhD student in the group of Prof. Helmchen in Zurich.

Melody Tong
Undergraduate Researcher 2017 | Harvard College Class of '18
Melody was co-mentored by Mackenzie and Nao Uchida. Her thesis work was focused on characterizing a rapidly learned freely-moving reaching & pulling task in mice.
She is now attending medical school at NYU.  

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News


News


News


News!
The laboratory will be moving to The Swiss Federal Institute of Technology, Lausanne (EPFL) in August 2020! We will be at Campus Biotech in Geneva. We will continue to integrate motor learning, artificial intelligence, & neurological disease-focused research with the generous support of the Bertarelli Foundation. Prof. Mackenzie Mathis was appointed as the Bertarelli Foundation Chair of Integrative Neuroscience.

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June 2019: Bloomberg Businessweek Magazine covered work in our lab!

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DeepLabCut 2.0 is published in Nature Protocols! Congratulations to Tanmay, Alex, Mackenzie & co-authors. Full python package, GUIs, 3D tools and more: https://www.nature.com/articles/s41596-019-0176-0 Plus, our team got the cover!

“A running cheetah with DeepLabCut Image of a cheetah ‘in the wild’ with markerless tracking of user-defined parts made with DeepLabCut, an open-source toolbox for deep-learning-based animal-pose estimation provided by Nath et al.”

Jan 2019: We hosted a DeepLabCut workshop! Scientists from across the US, CAN & UK joined us for a hands-on tutorial on how to use the deep learning toolbox.

Kai Sandbrink (masters student) joins the lab!

Nov 2018: A new preprint on using DeepLabCut is posted, Congrats to Tanmay & Alexander!

Our work on extensions to DeepLabCut was accepted to Cosyne 2019, and Alex’s Team presentation on “deep learning in motor neuroscience” is accepted to NCM 2019!

Sept 2018: Adrian receives his master’s degree! Congrats, Adrian! We wish you the best in Zurich!

August 2018: Our work on building the DeepLabCut toolbox, a deep learning method to perform markerless pose estimation was published in Nature Neuroscience, congrats to Alexander Mathis and co-authors!: rdcu.be/4Rep

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NVIDIA Developer Blog highlights DeepLabCut! https://news.developer.nvidia.com/ai-enables-markerless-animal-tracking/

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July 2018: Our preprint on DeepLabCut was covered by The Atlantic!  We are very happy that Ed Young was able to talk to some of the earlier adopters of DeepLabCut as well. For more information, see our page on DeepLabCut
Gary Kane, PhD (Postdoctoral fellow) joins the lab! 

June 2018: Our first paper from the lab is accepted! Stay tuned!

April 2018: Our first preprint from the lab, in collaboration with Matthias Bethge, is up on arXiv (check out our abstract page)!

Feb/March 2018: Congratulations to Melody Tong on completing her senior thesis! Adrian Hoffmann (masters student) joins the lab!

Jan 2018: Tanmay Nath, PhD (Postdoctoral fellow) joins the lab!

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Dec 2017: NVIDIA GPU Grant awarded to the lab! We thank NVIDIA Corporation for supporting our research.

September 1st, 2017: The lab doors are open!

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Funding


Funding


Funding:

We gratefully acknowledge the funding sources that make our research possible:



2017 - '22 | Rowland Fellowship to M. Mathis

2019 | Hardware grant from The Imaging Source, LLC (read more here)

2018 - ‘19 | Mind, Brain Behavior Faculty Award

2017 | NVIDIA GPU Grant Award

2017 | WATB/Project ALS - Postdoctoral Fellowship to M. Mathis

2013 - '17 | NSF Graduate Research Fellowship to M. Mathis
 

Affiliations:

The Rowland Institute at Harvard
Mind Brain Behavior - Interfaculty Initiative
Harvard Brain Science Initiative

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