Talmo Lab

Research

Our lab leverages deep learning and computer vision to study complex biological systems by building novel computational tools. Our core research areas of interest include:

Computational ethology

We develop methods for pose estimation and tracking to quantify animal behavior.

To help others make use of this technology, we created SLEAP: an open-source framework for the entire multi-animal pose tracking workflow.

Complex morphology phenotyping

We develop tools to quantify traits in complex morphologies such as plant root systems. We are applying these technologies to solve climate change in collaboration with experimental labs in the Salk Harnessing Plants Initiative.

Neuro-AI modeling

We are interested in exploring how artificial neural networks (ANNs) can be used as models of biological neural circuits. To do this, we combine agent-based modeling with imitation learning to take advantage of motion capture data to constrain our models. This work aims to improve our understanding of both brains and ANNs.

See below for a list of recent publications from the lab.

2022

Talmo D. Pereira, Nathaniel Tabris, Arie Matsliah, David M. Turner, Junyu Li, Shruthi Ravindranath, Eleni S. Papadoyannis, Edna Normand, David S. Deutsch, Z. Yan Wang, Grace C. McKenzie-Smith, Catalin C. Mitelut, Marielisa Diez Castro, John D’Uva, Mikhail Kislin, Dan H. Sanes, Sarah D. Kocher, Samuel S.-H. Wang, Annegret L. Falkner, Joshua W. Shaevitz, Mala Murthy
Nature Methods  ·  01 Apr 2022
Gabriella E. C. Gall, Talmo D. Pereira, Alex Jordan, Yasmine Meroz
Plant Methods  ·  20 Feb 2022
Kevin Luxem, Jennifer J. Sun, Sean P. Bradley, Keerthi Krishnan, Talmo D. Pereira, Eric A. Yttri, Jan Zimmermann, Mark Laubach
arXiv  ·  01 Jan 2022

2021

Z Yan Wang, Grace C. McKenzie-Smith, Weijie Liu, Hyo Jin Cho, Talmo Pereira, Zahra Dhanerawala, Joshua W. Shaevitz, Sarah D. Kocher
bioRxiv  ·  17 Dec 2021
Philippe Bourrianne, Stanley Chidzik, Daniel Cohen, Peter Elmer, Thomas Hallowell, Todd J. Kilbaugh, David Lange, Andrew M. Leifer, Daniel R. Marlow, Peter D. Meyers, Edna Normand, Janine Nunes, Myungchul Oh, Lyman Page, Talmo Periera, Jim Pivarski, Henry Schreiner, Howard A. Stone, David W. Tank, Stephan Thiberge, Christopher Tully,
medRxiv  ·  14 Jun 2021

2020

David Deutsch, Diego Pacheco, Lucas Encarnacion-Rivera, Talmo Pereira, Ramie Fathy, Jan Clemens, Cyrille Girardin, Adam Calhoun, Elise Ireland, Austin Burke, Sven Dorkenwald, Claire McKellar, Thomas Macrina, Ran Lu, Kisuk Lee, Nico Kemnitz, Dodam Ih, Manuel Castro, Akhilesh Halageri, Chris Jordan, William Silversmith, Jingpeng Wu, H Sebastian Seung, Mala Murthy
eLife  ·  23 Nov 2020
Talmo D. Pereira, Joshua W. Shaevitz, Mala Murthy
Nature Neuroscience  ·  09 Nov 2020
Jessica M Jones, William Foster, Colin R Twomey, Justin Burdge, Osama M Ahmed, Talmo D Pereira, Jessica A Wojick, Gregory Corder, Joshua B Plotkin, Ishmail Abdus-Saboor
eLife  ·  06 Aug 2020
Adam S. Charles, Benjamin Falk, Nicholas Turner, Talmo D. Pereira, Daniel Tward, Benjamin D. Pedigo, Jaewon Chung, Randal Burns, Satrajit S. Ghosh, Justus M. Kebschull, William Silversmith, Joshua T. Vogelstein
Annual Review of Neuroscience  ·  08 Jul 2020

2018

Talmo D. Pereira, Diego E. Aldarondo, Lindsay Willmore, Mikhail Kislin, Samuel S.-H. Wang, Mala Murthy, Joshua W. Shaevitz
Nature Methods  ·  20 Dec 2018
Aleksandra Badura, Jessica L Verpeut, Julia W Metzger, Talmo D Pereira, Thomas J Pisano, Ben Deverett, Dariya E Bakshinskaya, Samuel S-H Wang
eLife  ·  20 Sep 2018
Jan Clemens, Philip Coen, Frederic A. Roemschied, Talmo D. Pereira, David Mazumder, Diego E. Aldarondo, Diego A. Pacheco, Mala Murthy
Current Biology  ·  01 Aug 2018
A. Giovannucci, E.A. Pnevmatikakis, B. Deverett, T. Pereira, J. Fondriest, M.J. Brady, S.S.-H. Wang, W. Abbas, P. Parés, D. Masip
Journal of Neuroscience Methods  ·  01 Apr 2018
Gecia Bravo Hermsdorff, Talmo Pereira, Yael Niv
Springer Proceedings in Complexity  ·  01 Jan 2018

2017

Talmo D. Pereira, Mala Murthy
Neuron  ·  01 Aug 2017
Andrea Giovannucci, Aleksandra Badura, Ben Deverett, Farzaneh Najafi, Talmo D Pereira, Zhenyu Gao, Ilker Ozden, Alexander D Kloth, Eftychios Pnevmatikakis, Liam Paninski, Chris I De Zeeuw, Javier F Medina, Samuel S-H Wang
Nature Neuroscience  ·  20 Mar 2017

2016

Elizabeth T. Hobbs, Talmo Pereira, Patrick K. O’Neill, Ivan Erill
Algorithms for Molecular Biology  ·  08 Jul 2016