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Published 20 hours ago • verified publisher icon DeepLabCut

Body parts not being displayed in Napari GUI when trying to label frames

Open thewangshu opened this issue 6 months ago • 5 comments

Hi, these are the necessary specs. Kindly let me know if you would require anything else that would help you resolve this bug.

OS: Windows 10 GPU : Nvidia GeForce RTX 3090 Memory: 128 GB DLC Version: 2.3.9 Python Version: 3.9.0 Napari Version: 0.4.18 Matplotlib version: 3.5.2 Numpy version: 1.23.4

Initially even labelling frames was a problem as Napari was not loading but after successfully installing the napari-deeplabcut and selecting it as well, the body parts are not being displayed.

I'm aware that this similar issue has been faced by others as well and the fixes provided in terms of updating the napari version and reinstalling DLC have all been attempted by me already. I even tried dragging and pasting the config.yaml file into the napari canvas (by running anaconda prompt without admin privileges) but that did not yield anything either. I am still left with no body parts being showing in the napari gui. Please find below a screenshot of the anaconda prompt as well as the napari gui. Any help would be hugely appreciated. I also tried reinstalling DLC in the hope that it would fix the error and here is a list of the things it reinstalled:

Requirement already satisfied: deeplabcut==2.3.9 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut[gui]==2.3.9) (2.3.9)
Requirement already satisfied: dlclibrary>=0.0.6 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.0.6)
Requirement already satisfied: filterpy>=1.4.4 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.4.5)
Requirement already satisfied: ruamel.yaml>=0.15.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.18.6)
Requirement already satisfied: imgaug>=0.4.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.4.0)
Requirement already satisfied: imageio-ffmpeg in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.5.1)
Requirement already satisfied: numba>=0.54 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.60.0)
Requirement already satisfied: matplotlib!=3.7.0,!=3.7.1,>=3.3 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (3.5.2)
Requirement already satisfied: networkx>=2.6 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (3.2.1)
Requirement already satisfied: numpy>=1.18.5 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.23.4)
Requirement already satisfied: pandas!=1.5.0,>=1.0.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (2.2.2)
Requirement already satisfied: scikit-image>=0.17 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.24.0)
Requirement already satisfied: scikit-learn>=1.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.5.1)
Requirement already satisfied: scipy>=1.9 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.13.1)
Requirement already satisfied: statsmodels>=0.11 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.14.2)
Requirement already satisfied: tables>=3.7.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (3.9.2)
Requirement already satisfied: torch<=1.12 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.12.0)
Requirement already satisfied: tensorpack>=0.11 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.11)
Requirement already satisfied: tf-slim>=1.1.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.1.0)
Requirement already satisfied: tqdm in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (4.66.5)
Requirement already satisfied: pyyaml in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (6.0.2)
Requirement already satisfied: Pillow>=7.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (10.4.0)
Requirement already satisfied: pyside6<6.3.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut[gui]==2.3.9) (6.3.1)
Requirement already satisfied: qdarkstyle==3.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut[gui]==2.3.9) (3.1)
Requirement already satisfied: napari-deeplabcut>=0.2.1.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from deeplabcut[gui]==2.3.9) (0.2.1.7)
Requirement already satisfied: qtpy>=1.9 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from qdarkstyle==3.1->deeplabcut[gui]==2.3.9) (2.4.1)
Requirement already satisfied: huggingface-hub in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from dlclibrary>=0.0.6->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.24.5)
Requirement already satisfied: six in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from imgaug>=0.4.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.16.0)
Requirement already satisfied: opencv-python in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from imgaug>=0.4.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (4.10.0.84)
Requirement already satisfied: imageio in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from imgaug>=0.4.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (2.35.0)
Requirement already satisfied: Shapely in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from imgaug>=0.4.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (2.0.5)
Requirement already satisfied: cycler>=0.10 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from matplotlib!=3.7.0,!=3.7.1,>=3.3->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from matplotlib!=3.7.0,!=3.7.1,>=3.3->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (4.53.1)
Requirement already satisfied: kiwisolver>=1.0.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from matplotlib!=3.7.0,!=3.7.1,>=3.3->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.4.5)
Requirement already satisfied: packaging>=20.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from matplotlib!=3.7.0,!=3.7.1,>=3.3->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (24.1)
Requirement already satisfied: pyparsing>=2.2.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from matplotlib!=3.7.0,!=3.7.1,>=3.3->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (3.1.2)
Requirement already satisfied: python-dateutil>=2.7 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from matplotlib!=3.7.0,!=3.7.1,>=3.3->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (2.9.0.post0)
Requirement already satisfied: dask-image in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (2024.5.3)
Requirement already satisfied: napari==0.4.18 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.4.18)
Requirement already satisfied: natsort in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (8.4.0)
Requirement already satisfied: opencv-python-headless in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (4.10.0.84)
Requirement already satisfied: appdirs>=1.4.4 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (1.4.4)
Requirement already satisfied: app-model<0.3.0,>=0.1.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.2.8)
Requirement already satisfied: cachey>=0.2.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.2.1)
Requirement already satisfied: certifi>=2018.1.18 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (2024.7.4)
Requirement already satisfied: dask!=2.28.0,>=2.15.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from dask[array]!=2.28.0,>=2.15.0->napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (2024.8.0)
Requirement already satisfied: jsonschema>=3.2.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (4.23.0)
Requirement already satisfied: lazy-loader>=0.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.4)
Requirement already satisfied: magicgui>=0.3.6 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.9.1)
Requirement already satisfied: napari-console>=0.0.6 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.0.9)
Requirement already satisfied: napari-plugin-engine>=0.1.9 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.2.0)
Requirement already satisfied: napari-svg>=0.1.7 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.2.0)
Requirement already satisfied: npe2>=0.5.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.7.7)
Requirement already satisfied: numpydoc>=0.9.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (1.5.0)
Requirement already satisfied: pint>=0.17 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.24.3)
Requirement already satisfied: psutil>=5.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (6.0.0)
Requirement already satisfied: psygnal>=0.3.4 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.11.1)
Requirement already satisfied: pydantic<2,>=1.9.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (1.10.17)
Requirement already satisfied: pygments>=2.6.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (2.18.0)
Requirement already satisfied: PyOpenGL>=3.1.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (3.1.7)
Requirement already satisfied: sphinx<5,>=4.3.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (4.5.0)
Requirement already satisfied: superqt>=0.4.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.6.7)
Requirement already satisfied: tifffile>=2020.2.16 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (2024.8.10)
Requirement already satisfied: toolz>=0.10.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.12.1)
Requirement already satisfied: typing-extensions>=4.2.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (4.12.2)
Requirement already satisfied: vispy<0.13,>=0.12.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.12.2)
Requirement already satisfied: wrapt>=1.11.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from napari==0.4.18->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (1.16.0)
Requirement already satisfied: llvmlite<0.44,>=0.43.0dev0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from numba>=0.54->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.43.0)
Requirement already satisfied: pytz>=2020.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from pandas!=1.5.0,>=1.0.1->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (2024.1)
Requirement already satisfied: tzdata>=2022.7 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from pandas!=1.5.0,>=1.0.1->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (2024.1)
Requirement already satisfied: shiboken6==6.3.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from pyside6<6.3.2->deeplabcut[gui]==2.3.9) (6.3.1)
Requirement already satisfied: PySide6-Essentials==6.3.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from pyside6<6.3.2->deeplabcut[gui]==2.3.9) (6.3.1)
Requirement already satisfied: PySide6-Addons==6.3.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from pyside6<6.3.2->deeplabcut[gui]==2.3.9) (6.3.1)
Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from ruamel.yaml>=0.15.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.2.8)
Requirement already satisfied: joblib>=1.2.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from scikit-learn>=1.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.4.2)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from scikit-learn>=1.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (3.5.0)
Requirement already satisfied: patsy>=0.5.6 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from statsmodels>=0.11->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.5.6)
Requirement already satisfied: numexpr>=2.6.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from tables>=3.7.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (2.10.1)
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Requirement already satisfied: termcolor>=1.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from tensorpack>=0.11->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (2.4.0)
Requirement already satisfied: tabulate>=0.7.7 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from tensorpack>=0.11->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.9.0)
Requirement already satisfied: msgpack>=0.5.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from tensorpack>=0.11->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.0.8)
Requirement already satisfied: msgpack-numpy>=0.4.4.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from tensorpack>=0.11->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.4.8)
Requirement already satisfied: pyzmq>=16 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from tensorpack>=0.11->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (26.1.0)
Requirement already satisfied: absl-py>=0.2.2 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from tf-slim>=1.1.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (2.1.0)
Requirement already satisfied: colorama in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from tqdm->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (0.4.6)
Requirement already satisfied: setuptools in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from imageio-ffmpeg->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (72.1.0)
Requirement already satisfied: ndindex>=1.4 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from blosc2>=2.3.0->tables>=3.7.0->deeplabcut==2.3.9->deeplabcut[gui]==2.3.9) (1.8)
Requirement already satisfied: pims>=0.4.1 in c:\users\bariklab\anaconda3\envs\deeplabcut\lib\site-packages (from dask-image->napari-deeplabcut>=0.2.1.2->deeplabcut[gui]==2.3.9) (0.7)
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