Awesome
DeepLabCut-Live! GUI <img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/1596193544929-NHMVMXPVEYZ6R4I45DSR/ke17ZwdGBToddI8pDm48kOHwsIwndRGCkvek0XAcW4ZZw-zPPgdn4jUwVcJE1ZvWEtT5uBSRWt4vQZAgTJucoTqqXjS3CfNDSuuf31e0tVH0wqgmu6zkAOZ3crWCtkmLcPIuzHaxU8QRzZwtrVtHupu3E9Ef3XsXP1C_826c-iU/DLCLIVEGUI_LOGO.png?format=750w" width="350" title="DLC-live GUI" alt="DLC LIVE! GUI" align="right" vspace = "100">
<a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
GUI to run DeepLabCut-live on a video feed, record videos, and record external timestamps.
Installation Instructions
Getting Started
Open DeepLabCut-live-GUI
In a terminal, activate the conda or virtual environment where DeepLabCut-live-GUI is installed, then run:
dlclivegui
Configurations
First, create a configuration file: select the drop down menu labeled Config
, and click Create New Config
. All settings, such as details about cameras, DLC networks, and DLC-live Processors, will be saved into configuration files so that you can close and reopen the GUI without losing all of these details. You can create multiple configuration files on the same system, so that different users can save different camera options, etc on the same computer. To load previous settings from a configuration file, please just select the file from the drop-down menu. Configuration files are stored at $HOME/Documents/DeepLabCut-live-GUI/config
. These files do not need to be edited manually, they can be entirely created and edited automatically within the GUI.
Set Up Cameras <img src= https://imagizer.imageshack.com/img924/626/acJhWD.png align="right">
To setup a new camera, select Add Camera
from the dropdown menu, and then click Init Cam
. This will be bring up a new window where you need to select the type of camera (see Camera Support), input a name for the camera, and click Add Camera
. This will initialize a new Camera
entry in the drop down menu. Now, select your camera from the dropdown menu and clickEdit Camera Settings
to setup your camera settings (i.e. set the serial number, exposure, cropping parameters, etc; the exact settings depend on the specific type of camera). Once you have set the camera settings, click Init Cam
to start streaming. To stop streaming data, click Close Camera
, and to remove a camera from the dropdown menu, click Remove Camera
.
Processor (optional)
To write custom Processors
, please see here. The directory that contains your custom Processor
should be a python module -- this directory must contain an __init__.py
file that imports your custom Processor
. For examples of how to structure a custom Processor
directory, please see here.
To use your processor in the GUI, you must first add your custom Processor
directory to the dropdown menu: next to the Processor Dir
label, click Browse
, and select your custom Processor
directory. Next, select the desired directory from the Processor Dir
dropdown menu, then select the Processor
you would like to use from the Processor
menu. If you would like to edit the arguments for your processor, please select Edit Proc Settings
, and finally, to use the processor, click Set Proc
. If you have previously set a Processor
and would like to clear it, click Clear Proc
.
Configure DeepLabCut Network
<img src= https://imagizer.imageshack.com/img923/9730/MNzr1J.png align="right">
Select the DeepLabCut
dropdown menu, and click Add DLC
. This will bring up a new window to choose a name for the DeepLabCut configuration, choose the path to the exported DeepLabCut model, and set DeepLabCut-live settings, such as the cropping or resize parameters. Once configured, click Update
to add this DeepLabCut configuration to the dropdown menu. You can edit the settings at any time by clicking Edit DLC Settings
. Once configured, you can load the network and start performing inference by clicking Start DLC
. If you would like to view the DeepLabCut pose estimation in real-time, select Display DLC Keypoints
. You can edit the keypoint display settings (the color scheme, size of points, and the likelihood threshold for display) by selecting Edit DLC Display Settings
.
If you want to stop performing inference at any time, just click Stop DLC
, and if you want to remove a DeepLabCut configuration from the dropdown menu, click Remove DLC
.
Set Up Session
Sessions are defined by the subject name, the date, and an attempt number. Within the GUI, select a Subject
from the dropdown menu, or to add a new subject, type the new subject name in to the entry box and click Add Subject
. Next, select an Attempt
from the dropdown menu. Then, select the directory that you would like to save data to from the Directory
dropdown menu. To add a new directory to the dropdown menu, click Browse
. Finally, click Set Up Session
to initiate a new recording. This will prepare the GUI to save data. Once you click Set Up Session
, the Ready
button should turn blue, indicating a session is ready to record.
Controlling Recording
If the Ready
button is selected, you can now start a recording by clicking On
. The On
button will then turn green indicating a recording is active. To stop a recording, click Off
. This will cause the Ready
button to be selected again, as the GUI is prepared to restart the recording and to save the data to the same file. If you're session is complete, click Save Video
to save all files: the video recording (as .avi file), a numpy file with timestamps for each recorded frame, the DeepLabCut poses as a pandas data frame (hdf5 file) that includes the time of each frame used for pose estimation and the time that each pose was obtained, and if applicable, files saved by the Processor
in use. These files will be saved into a new directory at {YOUR_SAVE_DIRECTORY}/{CAMERA NAME}_{SUBJECT}_{DATE}_{ATTEMPT}
- YOUR_SAVE_DIRECTORY : the directory chosen from the
Directory
dropdown menu. - CAMERA NAME : the name of selected camera (from the
Camera
dropdown menu). - SUBJECT : the subject chosen from the
Subject
drowdown menu. - DATE : the current date of the experiment.
- ATTEMPT : the attempt number chosen from the
Attempt
dropdown.
If you would not like to save the data from the session, please click Delete Video
, and all data will be discarded. After you click Save Video
or Delete Video
, the Off
button will be selected, indicating you can now set up a new session.
References:
If you use this code we kindly ask you to you please cite Kane et al, eLife 2020. The preprint is available here: https://www.biorxiv.org/content/10.1101/2020.08.04.236422v2