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DeepLabCut 3.0 - Updates to COLABs and Notebooks for the PyTorch Engine by n-poulsen · Pull Request #2868 · DeepLabCut/DeepLabCut · GitHub
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DeepLabCut 3.0 - Updates to COLABs and Notebooks for the PyTorch Engine #2868

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Merged
MMathisLab merged 18 commits into from
Feb 28, 2025
Merged

DeepLabCut 3.0 - Updates to COLABs and Notebooks for the PyTorch Engine #2868

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ba8569d
update openfield COLAB
Feb 7, 2025
a079aa5
updated COLAB_YOURDATA_TrainNetwork_VideoAnalysis and COLAB_maDLC_Tra…
Feb 7, 2025
f0c519c
fix ReID notebook
Feb 7, 2025
f67f24d
fix ReID notebook
Feb 7, 2025
6974baa
save predictions to destfolder
Feb 7, 2025
8a53a06
update superanimal notebook
Feb 7, 2025
3c3ca56
Merge branch 'pytorch_dlc' into niels/colabs_and_notebooks
Feb 7, 2025
9ac9290
fixed demo_data.py, Demo_labeledexample_MouseReaching.ipynb
Feb 7, 2025
db7c750
set default batch size to 8, fix notebooks
Feb 7, 2025
6e37654
updated notebooks
Feb 7, 2025
c2c9a81
Merge branch 'pytorch_dlc' into niels/colabs_and_notebooks
n-poulsen Feb 7, 2025
bf0ff83
fix edited config
Feb 7, 2025
ee50925
fix edited config
Feb 7, 2025
d9a669f
fix edited config
Feb 7, 2025
e3c40e4
Merge branch 'pytorch_dlc' into niels/colabs_and_notebooks
Feb 14, 2025
9412886
update 3mice demo
Feb 14, 2025
c6edd9e
install deeplabcut through prerelease
Feb 28, 2025
c9ff454
Merge branch 'pytorch_dlc' into niels/colabs_and_notebooks
MMathisLab Feb 28, 2025
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12 changes: 10 additions & 2 deletions deeplabcut/create_project/demo_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,15 @@
from pathlib import Path

import deeplabcut
from deeplabcut.core.engine import Engine
from deeplabcut.utils import auxiliaryfunctions


def load_demo_data(config, createtrainingset=True):
def load_demo_data(
config: str,
createtrainingset: bool = True,
engine: Engine = Engine.PYTORCH,
):
"""
Loads the demo data -- subset from trail-tracking data in Mathis et al. 2018.
When loading, it sets paths correctly to run this project on your system
Expand All @@ -29,6 +34,9 @@ def load_demo_data(config, createtrainingset=True):
createtrainingset : bool
Boolean variable indicating if a training set shall be created.

engine: Engine
The Engine to create the training set for if a training set shall be created.

Example
--------
>>> deeplabcut.load_demo_data('config.yaml')
Expand All @@ -40,7 +48,7 @@ def load_demo_data(config, createtrainingset=True):
transform_data(config)
if createtrainingset:
print("Loaded, now creating training data...")
deeplabcut.create_training_dataset(config, num_shuffles=1)
deeplabcut.create_training_dataset(config, num_shuffles=1, engine=engine)


def transform_data(config):
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2 changes: 1 addition & 1 deletion deeplabcut/pose_estimation_pytorch/config/base/base.yaml
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Expand Up @@ -20,7 +20,7 @@ runner:
save_epochs: 25
save_optimizer_state: false
train_settings:
batch_size: 1
batch_size: 8
dataloader_workers: 0
dataloader_pin_memory: false
display_iters: 500
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6 changes: 5 additions & 1 deletion examples/COLAB/COLAB_3miceDemo.ipynb
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Expand Up @@ -16,18 +16,22 @@
"id": "TGChzLdc-lUJ"
},
"source": [
"# DeepLabCut 2.2 Toolbox Demo on 3 mice data\n",
"# DeepLabCut 2.2+ Toolbox Demo on 3 mice data\n",
"![alt text](https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/1628250004229-KVYD7JJVHYEFDJ32L9VJ/DLClogo2021.jpg?format=1000w)\n",
"\n",
"https://github.com/DeepLabCut/DeepLabCut\n",
"\n",
"Note: this Colab notebook was written to accompany the Nature Methods publication [_Multi-animal pose estimation, identification and tracking with DeepLabCut_](https://www.nature.com/articles/s41592-022-01443-0) with the TensorFlow engine. To learn about DeepLabCut 3.0+ and the PyTorch engine, you can check out our other notebooks (such as [`COLAB_YOURDATA_maDLC_TrainNetwork_VideoAnalysis.ipynb`](https://github.com/DeepLabCut/DeepLabCut/blob/main/examples/COLAB/COLAB_YOURDATA_maDLC_TrainNetwork_VideoAnalysis.ipynb)).\n",
"\n",
"### This notebook illustrates how to use COLAB for a multi-animal DeepLabCut (maDLC) Demo 3 mouse project:\n",
"\n",
"- load our mini-demo data that includes a pretrained model and unlabeled video.\n",
"- analyze a novel video.\n",
"- assemble animals and tracklets.\n",
"- create quality check plots and video.\n",
"\n",
"### To create a full maDLC pipeline please see our full docs: https://deeplabcut.github.io/DeepLabCut/README.html\n",
"\n",
"- Of interest is a full how-to for maDLC: https://deeplabcut.github.io/DeepLabCut/docs/maDLC_UserGuide.html\n",
"- a quick guide to maDLC: https://deeplabcut.github.io/DeepLabCut/docs/tutorial.html\n",
"- a demo COLAB for how to use maDLC on your own data: https://github.com/DeepLabCut/DeepLabCut/blob/main/examples/COLAB/COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb\n",
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