DeepLabCut 🦄
@DeepLabCut
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Python package for markerless pose estimation 4 animals (including humans) | free, open code | dev by @mwmathislab @amathislab
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🌎 Home Page:
📚Docs:
🛠️ Install: pip install 'deeplabcut[gui,tf]'
🐿 Model Zoo:
∞ Learn DeepLabCut - Free Online Course:
👩🏾💻👨💻 DeepLabCut AI Residency:
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🔥 multi-animal DeepLabCut™ is out (rc1)! 🥳
Interested in multi-animal tracking, identity leveraged + high perf. pose estimation? We thought so...
📘 PREPRINT by
@jessy_lauer
et al:
📝 BLOG POST:
💻 CODE:
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🎉DeepLabCut 2.2-beta: multi-animal pose estimation & tracking 🎉
🐭🐭🐭 Release note:
🕊️🕊️🕊️ work from the DLC2.2 core-devs:
@TrackingPlumes
@jessy_lauer
@TrackingActions
✨ 𝚙𝚒𝚙 𝚒𝚗𝚜𝚝𝚊𝚕𝚕 𝚍𝚎𝚎𝚙𝚕𝚊𝚋𝚌𝚞𝚝==𝟸.𝟸.𝚋𝟻 ✨
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📣
#ma
@DeepLabCut
is out in
@NatureMethods
!
We bring you an end-to-end high performance solution to multi-animal tracking.
✅1 line install 𝚙𝚒𝚙 𝚒𝚗𝚜𝚝𝚊𝚕𝚕 '𝚍𝚎𝚎𝚙𝚕𝚊𝚋𝚌𝚞𝚝[𝚐𝚞𝚒]'
✅use a full GUI, or only 7 lines of code...
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📢 1/2 one of the bigger
#deeplabcut
2.0 package updates!📢 2.0.7 is now out 🎉 Lots of updates, new GUI features, new plotting tools ... read more here: --->>> pip install deeplabcut==2.0.7
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a WIP , but as many students might find themselves doing remote work this summer, we will have self-paced modules (free, of course) on
#deeplearning
w/
#deeplabcut
:
✨ "Got Behavior? Get Poses ... " ✨
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🥳
#teamDLC
is delighted to present our Primer on Motion Capture with Deep Learning in
@NeuroCellPress
!
📑 want to know more about neural networks, optimization, data augmentation?
📈 pitfalls to avoid?
Paper:
Complete w/code:
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🥳 multi-animal DeepLabCut (
#maDLC
) has been updated!
Still in beta mode, but fully functional and community feedback is appreciated. 🥰
💫 pip install deeplabcut==2.2b6 💫
📣 read the release statement:
#DeepLabCut
#maDeepLabCut
🤠🎶🐜⬇️
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🚨Please apply! Come spend the summer with us in beautiful Geneva learning, developing, and shaping the future of next-gen behavioral analysis!
💜✨ fully paid positions (+travel funding)= nothing to loose!
the
#DeepLabCutAI
Residency Program is open for applications!
✨Lets change DEI in computer science
💰fully paid residency program
✅empowering next-gen leaders in behavioral analysis
🔥platinum supporter
@cziscience
; sponsors:
@NVIDIAAI
@EPFL_ELLIS_unit
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😍 deeplabcut 2.1.6+ is up! It's fully backwards compatible, and has several quality of life things (incl python 3.7compatibility). Read more here: run: 'pip install --upgrade deeplabcut' in your conda env. Now run like this little guy to go upgrade 💜
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✅ New stable release: DeepLabCut 2.2 🦄
Note:
Blog:
⭐️We highly recommend updating!
💜This is the biggest/best jump for DLC in a year 🔥
🙏Huge thanks to the team & contributors
Now the team is on a much deserved vacation ...
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#DLCProTip
: all the code to make the pretty figures from our recent
@naturemethods
paper is all open source!
📖:
💻:
🎉Main and suppl. figures have a
@ProjectJupyter
notebook! Tools include
@matplotlib
@numpy_team
@pandas_dev
💜
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🎉DLC 2.1.5 is up!! Minor but useful changes, including new GUI functions, faster dataset creation, & our 1st release with new CZI DLC Fellow, Jessy! Read more here: It's backwards compatible, so don't be afraid to upgrade! pip install deeplabcut==2.1.5 😎
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💜🔥 2.1 is released!!! Now supporting 8 networks, multi-augmentation types, a whole new Project Manager GUI, plus many more updates -5K lines added! Massive thanks to the team:
@meet10may
@trackingplumes
@TrackingActions
demo:
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📢 2.0.9 is released!!! new functions: built in video downsampling & cropping, multiple body pts, new data augmentation with tensorpack support, ..., new docs, check it out! 💜 thanks for great user contributions! as always, "pip install deeplabcut==2.0.9"
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🎉 𝞪 plugin release of the 🏝
@napari_imaging
+
#DeepLabCut
annotation tool!
- way faster labeling & refinement
- drag&drop your labeled-data subfolders into the workspace and go
Thanks to
@cziscience
for funding this plugin & napari devs-amazing tool💜
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It's May - that means it's definitely time for DLC2.2 ....
#maDeepLabCut
truly coming soon🥳 (thanks to the alpha testers out there this week putting it through it's paces ...)
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🥂MAJOR news!!
We received funding from
@cziscience
#EOSS
to support
#DeepLabCut
in 2021!!! We can't even put into words how happy & grateful we are.
Want to see where we are going in 2021?
#teamDLC
@EPFL
@CIS_EPFL
@Brainmind_EPFL
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🎉🎂🥂
#DeepLabCut
, the paper, is 2 yrs old!
@NatureNeuro
! With over 350 citations already, it’s been an amazing ride with you all—looking forward to many more years 🥰, also hopefully w/ur help! We will be on GitHub Sponsors!🥳 more info coming soon!
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🤗 We think it’s time for a challenge/friendly competition ! 🪄
Reply below with your best
#deeplabcut
video/gif (tag
@depelabcut
) and our dev team will pick a few winners for some awesome DLC Swag! Tweet/Toot 🐘by May 5th 💜
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🎉one of the new features in the soon-to-be-released update is that it's now very easy to add any "skeleton" and a history of points! More details coming soon! 🥳
#DeepLabCut
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✅ 𝚙𝚒𝚙 𝚒𝚗𝚜𝚝𝚊𝚕𝚕 '𝚍𝚎𝚎𝚙𝚕𝚊𝚋𝚌𝚞𝚝[𝚐𝚞𝚒]'==𝟸.𝟸𝚛𝚌𝟸
New features, new upgrades, definitely update 🥳 and read all about it on the blog!
TL;DR: If you're using or interesting in leveraging visual identity, this one is especially for you!
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Did someone say dogs? 🐶
✨ Introducing the DeepLabCut Model Zoo ✨
A growing collection of trained models for you to immediately use - no training required, no installation required (see below)! 🐕🐵🐈🐕🧍🐭
#openscience
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👀 it’s an exciting day! We released the first release candidate for 2.3 🔥
- a whole new GUI awaits you, and we await your feedback!
- Welcome to the world, our first full
@napari_imaging
+ PySide2 product!
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🎃Spooky times with
#DeepLabCut
, Starring Jack Skellington in 'The Nightmare Before Christmas' by
@TimWBurton
species: Skeleton💀
tracking: DLC
behavior detected: spooky👻😈
Happy Halloween🎃 Everyone!
🎥by
@TheVetFuturist
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*NEW* deeplabcut release is out!
𝚙𝚒𝚙 𝚒𝚗𝚜𝚝𝚊𝚕𝚕 '𝚍𝚎𝚎𝚙𝚕𝚊𝚋𝚌𝚞𝚝[𝚐𝚞𝚒]'==𝟸.𝟸.𝟶.𝟹
7 new contributors 🙏, big improvements ✅, simplified workflow for aspects of maDLC 💜 (more soon!), + a lot more: You don't want to miss this one ✨🎉
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🥳Happy Birthday
#DeepLabCut
! Paper & code was put onto arXiv 3 years ago:
Of course, underlying code has changed, as we aim to always bring you usable, top performing DNNs & tools to push your science!
This month we hit 200K downloads & 700 citations!🥰
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🥳Thanks to all the developers, contributors, and users, DeepLabCut has been awarded it's first (ever) funding - from
@cziscience
as an essential open source tool for science! We are so grateful!
@trackingactions
@TrackingPlumes
#Opensource
software is essential to science—that’s why we’re supporting 42 open source tools that accelerate biomedical research and serve the larger community. Learn about the grantees
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#DeepLabCut
2.0.5 is released! 🎊 Lots of great updates & new user functions + MacOS support! 💻 Check it out: Here is a new GUI to manually crop + grab frames (or a range of frames). There is also a similar new GUI for manual extraction of outlier frames!
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almost to 1K stars on GitHub! 😍 thank you all for the support of this project!
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🥳𝗗𝗟𝗖-𝗟𝗶𝘃𝗲! fast, low-latency posture-based feedback! new python pkgs PLUS integration into
-
@bonsai_rx
- Autopilot
- a new DLC-Live! GUI
Kane et al
@gkneuro
,
@glopesdev
,
@json_dirs
@TrackingPlumes
@TrackingActions
📜
📹
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#DeepLabCut
2.0.6 is up! 🥳 Check out the latest code: --> including easier application of filtering to output data, new GUIs + GUI updates, new docs, & more ...
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#DLCsneakPeek
👀... real-time DeepLabCut from our team coming soon: fast, low-latency, flexible (many ways to interact with it and build on it, plus ready-made solutions for plug&play DLC) .... ready for it?
#𝗗𝗟𝗖𝗟𝗶𝘃𝗲!😎
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alpha testing ✅ gearing up for the beta public release
#maDeepLabCut
😎
✨New feature to highlight: a new "skeleton" connector - since our new networks use the skeleton to train, you can draw them simply vs. typing into config.yaml 💜 (data from
@BalintZKacsoh
!)
#antsoftwitter
?
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🥳 Happy birthday, DeepLabCut!
Our first preprint and code was released 2 years ago today 🥰. Thanks to all the great users for making this a lab-changing adventure for many of us!
@arxiv_cscv
and then published in
@NatureNeuro
as
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🥳
#DeepLabCut
's latest is up! (our 1st release from
@EPFL
🇨🇭!)
𝚙𝚒𝚙 𝚒𝚗𝚜𝚝𝚊𝚕𝚕 𝚍𝚎𝚎𝚙𝚕𝚊𝚋𝚌𝚞𝚝==𝟸.𝟸𝚋𝟾
release note:
*tracklet improvements, bug fixes, new features!
We rec'd all users upgrade
@jessy_lauer
@TrackingPlumes
@TrackingActions
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🎉 we have some news: we launched a DLC Blog! ✅
A dedicated place for you to get the latest code release announcements, user highlights, and important notices for beta upcoming code releases (and to get your feedback!)
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Happy weekend all!
#Caturday
🐈⬛🐈 meets
#DeepLabCut
⬇️
DeepLabCut Model Zoo is live!
Working from home? try out
#deeplabcut
on your favorite pets, no need to install anything.
Use custom DeepLabCut Model Zoo
@GoogleColab
Notebook:
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#DeepLabCut
is an open-source tool for
#pose_estimation
built on the
#Python3
stack and feeds into open-source analysis and behavioral tools. We aimed to make
#deep_learning
highly accessible w/o exp.
<- all the papers, docs, code, videos, workshops, etc
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✨News: we will be hosting a
#DeepLabCut
webinar in Nov! Stay tuned/follow for updates & a sign up soon!
What do you want to hear about the most from lead devs,
@TrackingActions
&
@TrackingPlumes
? 🤩 Please post below!
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#maDeepLabCut
#protip
: the 'skeleton' is used for training, & this means connecting it is key! We built a new
@matplotlib
based GUI (& a
@scidrawio
🐭 to demo) how to (1) use more points, and (2) how to connect the skeleton!
📹
📖
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DeepLabCut is free but takes 💰to maintain & develop!
📣
#DeepLabCut
is now on GitHub Sponsors!!
Your 💸 goes directly to support it! Have a little left on your grant? Use us instead of $$$ software? Consider donating! And ⭐️the code 4 support 🙏🏼
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🐶🐕endorsed!! The latest version of
#deeplabcut
has a whole new gui, where
@napari_imaging
is the default platform! 🙌
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We are so excited for this merger! ❤️💜Our model export code will be up soon so you can simply export your trained model for an import into bonsai! (Below is the human prettained network) started at our dlc hackathon! Thx
@cziscience
Bonsai 2.5 + real-time DeepLabCut! You can now connect live tracking to your hardware in closed-loop. Install from: , DLC GPU install instructions at:
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🐁💜
#deeplabcut
+🦓🖤
#cebra
= 🔥
@mwmathislab
show you can use
@CEBRAai
with only neural data, only behavior data (
#CEBRA
supports loading your
@DeepLabCut
data 👀), and powerfully combine data for rich metrics & insights into neural population dynamics
New paper from
@TrackingActions
! I liked this one because neuroscience has seen huge advances in recording technologies and behavioral tracking, but it's not always clear what to do with all the data. This paper shows an elegant approach
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✅ New docs: and introducing the DeepLabCut CookBook!
📚 Check out the current recipes, and watch this space grow!
📣Plus, please contribute: have a non-doc'd way of using DLC? And easy-to-use guide? Please share it! 💜
💛made w/
#JupyterBook
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👀 The 🥇DLC paper is just over 4 years old 🎂, 415,000 code downloads, 97 code contributors 🔥, the top paper in
@NatureNeuro
in this time period by citations, and still providing top performance for animal pose estimation!
💕 Thank you DLC Community! 💕
Even more to come…
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🔥 DeepLabCut now supports the latest
@TensorFlow
2+! 🔥
📣 backwards compatible, easy to install, refactored and streamlined code! Big thanks to
@jessy_lauer
#teamDLC
, and
@cziscience
for funding this crucial code maintenance.
📖 see for how to upgrade!
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Stuck at home? New tutorial on using (free) GPUs for training and video inference w/
#DeepLabCut
on
@GoogleColab
- also extremely exciting to see that COLAB now has a paid version for *longer run times* (only 10/month)! 🥳😱🤩
#deeplearning
#gpus
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🤩💜👉 New funding awarded for building out a
@napari_imaging
plugin 💜❤️! A huge thank you to
@cziscience
for the incredible support!
BONUS: check out the *new* napari-DLC GUI now!
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Beautiful
#DeepLabCut
tracking and awesome science! 💜🧡💛
Researchers uncover the neuronal circuits that let fruit fly larvae control their speed and think this mechanism could help us understand locomotion in other limbed species.
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🥂🥳 We hit some big milestones this weekend!
#DeepLabCut
hit 500 citations!
stats:
#DLC
software hit 170,000 downloads!
Thanks to the wonderful users, contributors, journalists, & funders!
💜
#teamDLC
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🎉 a new version of 𝙳𝚎𝚎𝚙𝙻𝚊𝚋𝙲𝚞𝚝-𝙻𝚒𝚟𝚎! is released!
- docs, code improvements, plus a new simple benchmarking script that makes it easy to contribute your stats!
🖥️ install:
📖 paper:
👩💻code:
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#DLCProTip
: Did you know that this year we launched a free online course for learning to use
#DeepLabCut
?!
🥳 Click here to get started via the graphic:
or simply:
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Oh yeah - we love tracking
@MCHammer
too 🕺😎 🎤
#deeplearning
#tracking4science
#trackingsoftwarefans
#opensource
#deeplabcut
⏬
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And now the Nature Protocols paper to go along side it! Updated user guide and new benchmarking --> 2.0 is 2X the performance ;)
@NatureNews
@NatureProtocols
Full paper:
& free-to-read link:
📢 1/2 one of the bigger
#deeplabcut
2.0 package updates!📢 2.0.7 is now out 🎉 Lots of updates, new GUI features, new plotting tools ... read more here: --->>> pip install deeplabcut==2.0.7
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#maDLC
highlight time! 🥳
This incredible data is from
@valedisanto
&
@georgelauder
! It’s a really gorgeous and challenging dataset, but with our new nets we reach 96% purity!
#funFact
,
@nature
chatted with Valentina early on the get the scoop on
#maDLC
🔥 multi-animal DeepLabCut™ is out (rc1)! 🥳
Interested in multi-animal tracking, identity leveraged + high perf. pose estimation? We thought so...
📘 PREPRINT by
@jessy_lauer
et al:
📝 BLOG POST:
💻 CODE:
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🎉
#DLCAIResidency
-
@Nirelkadzo
&
#teamMegaDLC
🔥 The team hooked up 💚MegaDetector+DeepLabCut 💜 and deployed it on 🤗!
📚 Read about it in the
#cookbook
:
𐂐 And hey, it's live, go test it out!
@huggingface
App 🤗:
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🥳New release! Some major code unbundling, performance updates, GUI updates (new rotate+crop video fxn), EfficientNet models as *NEW* high-performance options in the GUI, plus full_cheetah in the zoo!
🔥new way to get it all:
pip install 'deeplabcut[gui]'
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Beautiful tracking! 💜🎉
Exciting collaboration, in which I could bring my
@DeepLabCut
expertise. During optogenetics-induced locomotion (i.e., "non-volitional"!), mice can still engage turning and braking behaviours. Thanks
#DimitriRyczko
for this opportunity.
#neuroscience
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Very cool use of
#DeepLabCut
! 🤹And, amazing motor skills!
Introducing the
@freemocap
system! A free, open-source framework for easy-to-use, low-cost markerless motion capture!
✨💀✨
The current iteration relies on
#anipose
,
#openpose
and
@DeepLabCut
. Animation via
@matplotlib
#opensource
#OpenScience
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the
#DeepLabCutAI
Residency Program is open for applications!
✨Lets change DEI in computer science
💰fully paid residency program
✅empowering next-gen leaders in behavioral analysis
🔥platinum supporter
@cziscience
; sponsors:
@NVIDIAAI
@EPFL_ELLIS_unit
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🐙👏 love it!!!
Using two layers of
@DeepLabCut
models to track the tips of
#octopus
arms in HD videos.
@MarineBiol_FHL
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they might not be easter bunnies, but the penguins wish you all a great holiday weekend... (image from a new 2.2 function coming soon ;). 🐧🐧🐧🐧🐧
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We are hiring! Are you a full stack software engineer who wants to work on an open source project?
#deeplabcut
is calling... contact us (emails at ) for more information!
#machinelearning
#deeplearning
#poseEstimation
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📣package update including model_export!
pip install deeplabcut==2.1.7
Want to freeze+store your TF weights for easy sharing and for real-time applications like in
@bonsai_rx
? Now you can! Also, you can download the trained human network for use at now!
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#DeepLabCut
has been used extensively for locomotor analysis and we wanted to highlight one awesome example from
@j_cregg
&
@KiehnLab
(
#BrainPrize
winner 2022!🎉)
📖- Now up on the blog!
🤩- Thanks Jared for the interview!
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🎉The 2nd annual DeepLabCut Workshop date is officially set! 🎉 Jan 15-16, 2020 at Harvard!
Application form: (application closes Dec 1st!)
More details:
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👋 Who's taking part in the
#DeepLabCut
2020 course?!
▶️ self-paced, and resources added often!
Check out the materials here, including NEW videos:
me!
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now I will!
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maybe later :)
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#SuperAnimal
is also very easy to use! Use it in the DLC GUI or just 1 line to run💜🥳
👀Just pass the video path and the model name: Mouse🐭 or Quadruped🐅:
deeplabcut . video_inference_superanimal ([ video_path ] , superanimal_name, video_adapt = True)
🐁🐘🐿🔥SuperAnimals for
#Pose
-No human labeling
- Video analysis on over 45 species with only 2 global classes of animal pose models
-If SA needs fine-tuning, its 10× more data efficient & 2X outperforms prior transfer learning
📝
@shaokaiyeah
et al
🧵⬇️
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📢
#deeplabcut
2.0.8 is up! 📢 utility-based updates () + **NEW** pre-trained network-based project: instantly analyze your human data without any training (even on Colab : ) 🎉👇 thanks to
@whoisBMH
for the dance moves 😎👇
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beautiful tracking of lemurs and mice with a real-time DeepLabCut! (plus nice real-time opto in VTA) 👏
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🔥 Apply to be a 2023 DLC AI Resident! Do you identify as underrepresented in CS &ML?
💜 Join us to learn next gen behavior, computer vision, & open source practices
😎 incredible speakers
📚 read & apply:
🚧deadline Dec 1st, 2022
please RT🙏
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🥳 New docs! A dedicated guide to using multi-animal pose estimation and tracking with
#DeepLabCut
is up! (plus many videos to go along with it)
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#DLCProTip
: in our latest release we have an advanced labeling feature for multi-camera data!
You can project epi-polar lines into the GUI image space so you are labeling the SAME points in 3D space! 🔥✅
^Super great contribution from the community!
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Hi new followers, thanks for joining! DeepLabCut allows for efficient measurement of animal behaviors! Using deep learning, we provide a toolbox to generate custom neural networks for your scientific needs - free, open source:
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👀
#deeplabcut
2.1sneak peek: a new Project Manager GUIto build and manage your DeepLabCut projects fully!
#teamDLC
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🥳 PS: Alongside 2.2b6 we also put out a *new* COLAB (
@GoogleColab
) notebook for training and analyzing videos on your multi-animal projects!
So, super easy install DLC-CPU on any computer, then simply move project folder to google drive and go! 😎
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👀 It's been a while since we made a stable release, here you go!
pip install deeplabcut==2.1.9
--> many exciting upgrades for all users
--> more exciting updates to come in 2.2 by Dec 2020 (let's end the year off right! 😍)
(video from )
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We are so flattered! Our preprint () has made it into the BioRxiv Top 15 of all-time in neuroscience by # of downloads! 😱 Thanks to all the awesome users (all user-generated content in videos below)!
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🥳 Come join us for the second edition of the DeepLabCut global Cajal course - online and local hubs across the 🌎🌍🌏, several hubs are led by former
#DLCAIResidents
!
Do you want to learn how to track poses, analyze what animals are doing, identify your favorite bear or link behavioral to neural data?
Join the hands-on, 5 day Cajal course from 6 to 10 November!
@Cajal_Training
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#dlcProTip
: building great models comes from great data. 10 highly different videos with 20 (diff) frames each is a MUCH better than 200 frames from 1 video.
Want to learn more? Read our primer on the principles of DNNs for MoCap:
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#protip
: as of 2.1 we added dynamic cropping to video analysis. If you animal is a small part of the frame (e.g. openfield assays, as shown below), this will help with analysis speed!!! Docs now added for this feature:
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Very nice tracking, and comes on an exciting day: 350,000 downloads!!
Congrats to the 80 code contributors and the larger community — this is your milestone!! 💪🙏🏼🥰
#openscience
#opencode
#betterresearch
The multi-camera rig is running! Mouse limb kinematics captured by CWRU student Keenan Hope. Markerless tracking and camera calibration were implemented with the
@DeepLabCut
and Anipose packages.
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1st Hackathon was a smashing success! Updates/blog post soon, but very excited about several projects we collectively made headway on! 🤩💜💪🏻
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Extra time on your hands? Analyze your old behavior videos!! Easy to go from old videos to data figures in a day with our easy to use free software package. Always nice to have behavior in your phd thesis :).
Check out how to get started:
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Wishing you a Happy New Year!
#teamDLC
thanks you for all your support this year. Your tweets, 💜, & ⭐️’s give us so much motivation and support, truly!
We look forward to making
#DeepLabCut
even better in 2021!
Have a fav.
#DLC
video? Post below!
🥰🐭🐒🦜🦇🐆🐮🐎🦦🦡🐿🦮
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💜 Our docs get an update! Inspired by some great suggestions we heard at the
@cziscience
#EOSSmtg
, we’ve done some organization and new extensions:
- plus new conda files with a super simple way to use: simply download from 🤩
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2/2 💡NEW features, such as transform your 2D camera views into 3D easily inside our package (using openCV and new functions)!
🥇 README:
🥈 3D
#DeepLabCut
video tutorial:
🥉 Jupyter Notebook 3D demo:
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