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Various scripts to support deeplabcut...
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DLC_2_MotionMapper
pupilTracking added pupilDLC.py Feb 4, 2019
Demo_loadandanalyzeDLCdata.ipynb Example notebook for loading data and roi analysis Jun 12, 2019
README.md Update README.md May 2, 2019
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convertDLC1TO2.py Update import file Nov 12, 2018
convertWin2Unix.py Hack for using colab with data labeled in windows... Jan 14, 2019
dlc_ubuntu18.yml ubuntu 18 conda environment as used for woods hole course Jun 19, 2019
installDLCandAnaconda.sh Installation... Jul 20, 2019
m3v1mp4DeepCut_resnet50_openfieldOct30shuffle1_15001.h5 Example notebook for loading data and roi analysis Jun 12, 2019
scale_analysis_oversubfolders.py Examples for scalable analysis Feb 10, 2019
scale_training_and_evaluation.py Update and rename scale_raining_and_evaluation.py to scale_training_a… May 9, 2019
testDLC.py Installation... Jul 20, 2019
time_in_each_roi.py Example notebook for loading data and roi analysis Jun 12, 2019

README.md

Image.sc forum

DeepLabCut-Utils

Various scripts to support DeepLabCut. Feel free to contribute your own analysis methods, and perhaps some short notebook of how to use it. Thanks!

Example scripts for automation of anlysis & training

These two scripts illustrate how to train, test and analyze videos for multiple projects automatically (scale_raining_and_evaluation.py) and how to analyze videos that are organized in subfolders automatically (scale_analysis_oversubfolders.py). Feel free to adjust them for your needs!

https://github.com/AlexEMG/DLCutils/blob/master/scale_analysis_oversubfolders.py https://github.com/AlexEMG/DLCutils/blob/master/scale_raining_and_evaluation.py

Contributed by Alexander Mathis

DLC1 to DLC 2 conversion code

This code allows you to import the labeled data from DLC 1 to DLC 2 projects. Note, it is not streamlined and should be used with care.

https://github.com/AlexEMG/DLCutils/blob/master/convertDLC1TO2.py

Contributed by Alexander Mathis

Running project created on Windows on Colaboratory

#UPDATE: as of Deeplabcut 2.0.4 onwards you no longer need to use this code! You can simply create the training set on the cloud and it will automatically convert your project for you.

Usage: change in lines 70 and 71 of https://github.com/AlexEMG/DLCutils/blob/master/convertWin2Unix.py

basepath='/content/drive/My Drive/DeepLabCut/examples/'

projectname='Reaching-Mackenzie-2018-08-30'

then run this script on colaboratory after uploading your labeled data to the drive. Thereby it will be converted to unix format, then create a training set (with deeplabcut) and proceed as usual...

Contributed by Alexander Mathis

Time spent of a body part in a particular region of interest (ROI)

https://github.com/AlexEMG/DLCutils/blob/master/time_in_each_roi.py

Contributed by Federico Claudi

Behavior clustering with MotionMapper

https://github.com/AlexEMG/DLCutils/tree/master/DLC_2_MotionMapper

Contributed by Mackenzie Mathis

Using DeepLabCut for USB-CGPIO feedback

paper: https://www.biorxiv.org/content/early/2018/11/28/482349

code: https://github.com/bf777/DeepCutRealTime

maintainer: Brandon Forys

A wrapper package for DeepLabCut2.0 for 3D videos (anipose)

code: https://github.com/lambdaloop/anipose

maintainer: Pierre Karashchuk

Pupil Tracking

Please direct inquires to the contributors/code-maintainers of that code. Note that the software(s) are provided "as is", without warranty of any kind, express or implied.

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