Welcome!

Contents
Welcome!
Installation: how to install DeepLabCut
Documentation: The DeepLabCut Process
DEMO the code
Why use DeepLabCut?
Get Assistance & be part of the DLC
Community :
News (and in the news):
 Documentation | Installation |
Home Page | Model Zoo |
News | Reporting Issues

Getting Assistance | ∞ DeepLabCut

Online Course | Publications |
DeepLabCut AI Residency

python version 3.10 downloads 848k

downloads/month 16k

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open issues 2% forum 2213 topics

chat on gitter DeepLabCut

Contributions Welcome

DeepLabCut is a toolbox for state-of-the-

art markerless pose estimation of animals
performing various behaviors. As long as you
can see (label) what you want to track, you
can use this toolbox, as it is animal and
object agnostic. Read a short development
and application summary below.

Please click the link above for all the

information you need to get started! Please
note that currently we support only Python
3.10+ (see conda files for guidance).

Developers Stable Release: very quick start

(Python 3.10+ required) to install
DeepLabCut with the PyTorch engine

Install PyTorch (select the desired

CUDA version if you want to use a
GPU): pip install torch
torchvision

Then, install pytables : conda install

-c conda-forge pytables==3.8.0

Finally, install DeepLabCut (with all

functions + the GUI): pip install
--pre "deeplabcut[gui]" or pip
install --pre "deeplabcut"
(headless version with PyTorch)!

To use the TensorFlow engine (requires

Python 3.10; TF up to v2.10 supported on
Windows, up to v2.12 on other platforms):
you’ll need to run pip install
"deeplabcut[gui,tf]" (which includes all
functions plus GUIs) or pip install
"deeplabcut[tf]" (headless version with
PyTorch and TensorFlow).

We recommend using our conda file, see

here or the new deeplabcut-docker
package.

Our docs walk you through using

DeepLabCut, and key API points. For an
overview of the toolbox and workflow for
project management, see our step-by-step at
Nature Protocols paper.

For a deeper understanding and more

resources for you to get started with Python
and DeepLabCut, please check out our free
online course!
http://DLCcourse.deeplabcut.org

pose tracking of single animals demo

Open in Colab

See more demos here. We provide data and

several Jupyter Notebooks: one that walks
you through a demo dataset to test your
installation, and another Notebook to run
DeepLabCut from the beginning on your own
data. We also show you how to use the code
in Docker, and on Google Colab.

In 2018, we demonstrated the capabilities for

trail tracking, reaching in mice and various
Drosophila behaviors during egg-laying (see
Mathis et al. for details). There is, however,
nothing specific that makes the toolbox only
applicable to these tasks and/or species. The
toolbox has already been successfully
applied (by us and others) to rats, humans,
various fish species, bacteria, leeches,
various robots, cheetahs, mouse whiskers
and race horses. DeepLabCut utilized the
feature detectors (ResNets + readout layers)
of one of the state-of-the-art algorithms for
human pose estimation by Insafutdinov et al.,
called DeeperCut, which inspired the name
for our toolbox (see references below). Since
this time, the package has changed
substantially. The code has been re-tooled
and re-factored since 2.1+: We have added
faster and higher performance variants with
MobileNetV2s, EfficientNets, and our own
DLCRNet backbones (see Pretraining boosts
out-of-domain robustness for pose
estimation and Lauer et al 2022). Additionally,
we have improved the inference speed and
provided both additional and novel
augmentation methods, added real-time, and
multi-animal support. In v3.0+ we have
changed the backend to support PyTorch.
This brings not only an easier installation
process for users, but performance gains,
developer flexibility, and a lot of new tools!
Importantly, the high-level API stays the
same, so it will be a seamless transition for
users ! We currently provide state-of-the-
art performance for animal pose estimation
and the labs (M. Mathis Lab and A. Mathis
Group) have both top journal and computer
vision conference papers.
Left: Due to transfer learning it requires little
training data for multiple, challenging
behaviors (see Mathis et al. 2018 for details).
Mid Left: The feature detectors are robust to
video compression (see Mathis/Warren for
details). Mid Right: It allows 3D pose
estimation with a single network and camera
(see Mathis/Warren). Right: It allows 3D pose
estimation with a single network trained on
data from multiple cameras together with
standard triangulation methods (see Nath*
and Mathis* et al. 2019).

DeepLabCut is embedding in a larger open-

source eco-system, providing behavioral
tracking for neuroscience, ecology, medical,
and technical applications. Moreover, many
new tools are being actively developed. See
DLC-Utils for some helper code.

Code contributors:
DLC code was originally developed by
Alexander Mathis & Mackenzie Mathis, and
was extended in 2.0 with the core dev team
consisting of Tanmay Nath (2.0-2.1), and
currently (2.1+) with Jessy Lauer and (2.3+)
Niels Poulsen. DeepLabCut is an open-
source tool and has benefited from
suggestions and edits by many individuals
including Mert Yuksekgonul, Tom Biasi,
Richard Warren, Ronny Eichler, Hao Wu,
Federico Claudi, Gary Kane and Jonny
Saunders as well as the 100+ contributors.
Please see AUTHORS for more details!

This is an actively developed package and we

welcome community development and
involvement.

Estimated
Response
Platform Goal Time

forum 2213 topics To ask Promptly

Tag: DeepLabCut help and
 support
questions

GitHub To report 2-3 days

DeepLabCut/Issues bugs and
code
issues
(we
encourage
you to
search
issues
first)

chat on gitter To discuss 2 days

with other
users,
share
ideas and
collaborate

GitHub To Promptly
DeepLabCut/Contributing contribute
your
expertise
and
experience

GitHub To learn N/A

DeepLabCut/Roadmap more
about our
journey

DeepLabCut To keep up Daily

with our
 latest
news and
updates

The DeepLabCut AI To come Annually

Residency Program and work
with us
next
summer

References & Citations:

Please see our dedicated page on how to
cite DeepLabCut and our suggestions
for your Methods section!

License:
This project is primarily licensed under the
GNU Lesser General Public License v3.0.
Note that the software is provided “as is”,
without warranty of any kind, express or
implied. If you use the code or data, please
cite us! Note, artwork (DeepLabCut logo) and
images are copyrighted; please do not take
or use these images without written
permission.

SuperAnimal models are provided for

research use only (non-commercial use).
Major Versions:
For all versions, please see here.

VERSION 3.0: A whole new experience with

PyTorch . While the high-level API remains
the same, the backend and developer
friendliness have greatly improved, along with
performance gains!

VERSION 2.3: Model Zoo SuperAnimals, and

a whole new GUI experience.

VERSION 2.2: Multi-animal pose estimation,

identification, and tracking with DeepLabCut
is supported (as well as single-animal
projects).

VERSION 2.0-2.1: This is the Python

package of DeepLabCut that was originally
released in Oct 2018 with our Nature
Protocols paper (preprint here). This package
includes graphical user interfaces to label
your data, and take you from data set
creation to automatic behavioral analysis. It
also introduces an active learning framework
to efficiently use DeepLabCut on large
experimental projects, and data
augmentation tools that improve network
performance, especially in challenging cases
(see panel b).

VERSION 1.0: The initial, Nature

Neuroscience version of DeepLabCut can be
found in the history of git, or here:
 DeepLabCut/DeepLabCut

:purple_heart: We released a major update,

moving from 2.x –> 3.x with the backend
change to PyTorch

:purple_heart: The DeepLabCut Model Zoo

launches SuperAnimals, see more here.

:purple_heart: DeepLabCut supports multi-

animal pose estimation! maDLC is out of
beta/rc mode and beta is deprecated, thanks
to the testers out there for feedback! Your
labeled data will be backwards compatible,
but not all other steps. Please see the new
2.2+ releases for what’s new & how to
install it, please see our new paper, Lauer et
al 2022, and the new docs on how to use it!

:purple_heart: We support multi-animal re-

identification, see Lauer et al 2022.

:purple_heart: We have a real-time package

available! http://DLClive.deeplabcut.org

June 2024: Our second DLC paper

‘Using DeepLabCut for 3D markerless
pose estimation across species and
behaviors’ in Nature Protocols has
surpassed 1,000 Google Scholar
citations!
May 2024: DeepLabCut was featured in
Nature: ‘DeepLabCut: the motion-
tracking tool that went viral’
January 2024: Our original paper
‘DeepLabCut: markerless pose
estimation of user-defined body parts
with deep learning’ in Nature
Neuroscience has surpassed 3,000
Google Scholar citations!
December 2023: DeepLabCut hit
600,000 downloads!
October 2023: DeepLabCut celebrates a
milestone with 4,000 in Github!
July 2023: The user forum is very active
with more than 1k questions and
answers: forum 2213 topics

May 2023: The Model Zoo is now fully

integrated into the DeepLabCut GUI,
making it easier than ever to access a
variety of pre-trained models. Check out
the accompanying paper: SuperAnimal
pretrained pose estimation models for
behavioral analysis by Ye et al.
December 2022: DeepLabCut hits
450,000 downloads and 2.3 is the new
stable release
August 2022: DeepLabCut hit 400,000
downloads
August 2021: 2.2 becomes the new
stable release for DeepLabCut.
July 2021: Docs are now at
https://deeplabcut.github.io/DeepLabCut
and we now include TensorFlow 2
support!
May 2021: DeepLabCut hit 200,000
downloads! Also, Our preprint on 2.2,
multi-animal DeepLabCut is released!
Jan 2021: Pretraining boosts out-of-
domain robustness for pose estimation
published in the IEEE Winter Conference
on Applications of Computer Vision. We
also added EfficientNet backbones to
DeepLabCut, those are best trained with
cosine decay (see paper). To use them,
just pass “ efficientnet-b0 ” to
“ efficientnet-b6 ” when creating the
trainingset!
Dec 2020: We released a real-time
package that allows for online pose
estimation and real-time feedback. See
DLClive.deeplabcut.org.
5/22 2020: We released 2.2beta5. This
beta release has some of the features of
DeepLabCut 2.2, whose major goal is to
integrate multi-animal pose estimation to
DeepLabCut.
Mar 2020: Inspired by suggestions we
heard at this weeks CZI’s Essential Open
Source Software meeting in Berkeley, CA
we updated our docs. Let us know what
you think!
Feb 2020: Our review on animal pose
estimation is published!
Nov 2019: DeepLabCut was recognized
by the Chan Zuckerberg Initiative (CZI)
with funding to support this project.
Read more in the Harvard Gazette, on
CZI’s Essential Open Source Software for
Science site and in their Medium post
Oct 2019: DLC 2.1 released with lots of
updates. In particular, a Project Manager
GUI, MobileNetsV2, and augmentation
packages (Imgaug and Tensorpack). For
detailed updates see releases
Sept 2019: We published two preprints.
One showing that ImageNet pretraining
contributes to robustness and a review
on animal pose estimation. Check them
out!
Jun 2019: DLC 2.0.7 released with lots of
updates. For updates see releases
Feb 2019: DeepLabCut joined twitter
DeepLabCut

Jan 2019: We hosted workshops for DLC

in Warsaw, Munich and Cambridge. The
materials are available here
Jan 2019: We joined the Image Source
Forum for user help: forum 2213 topics

Nov 2018: We posted a detailed guide

for DeepLabCut 2.0 on BioRxiv. It also
contains a case study for 3D pose
estimation in cheetahs.
Nov 2018: Various (post-hoc) analysis
scripts contributed by users (and us) will
be gathered at DLCutils. Feel free to
contribute! In particular, there is a script
guiding you through importing a project
into the new data format for DLC 2.0
Oct 2018: new pre-print on the speed
video-compression and robustness of
DeepLabCut on BioRxiv
Sept 2018: Nature Lab Animal covers
DeepLabCut: Behavior tracking cuts
deep
Kunlin Wei & Konrad Kording write a very
nice News & Views on our paper:
Behavioral Tracking Gets Real
August 2018: Our preprint appeared in
Nature Neuroscience
August 2018: NVIDIA AI Developer News:
AI Enables Markerless Animal Tracking
July 2018: Ed Yong covered DeepLabCut
and interviewed several users for the
Atlantic.
April 2018: first DeepLabCut preprint on
arXiv.org

Funding
We are grateful for the follow support
over the years! This software project was
supported in part by the Essential Open
Source Software for Science (EOSS)
program at Chan Zuckerberg Initiative
(cycles 1, 3, 3-DEI, 4), and jointly with
the Kavli Foundation for EOSS Cycle 6!
We also thank the Rowland Institute at
Harvard for funding from 2017-2020, and
EPFL from 2020-present.