Can't seem to get sleap_nn working on my Mac Intel

[srami0619]

Hello, I am trying to install the newest version of sleap on my Mac Intel by following the steps for pip installation on the installation guide. I am able to install sleap on a new conda environment and open the GUI, but when I try to run training, it says that sleap_nn is missing.

If you look at the top of my terminal output however, I'm sure I did install sleap with the sleap_nn package. I noticed the line,
"sleap 1.5.0 does not provide the extra 'nn'"
Where can I get the sleap_nn I need to run the training then? I could not find anything to solve this in the installation guide, so any help is greatly appreciated. Thank you!!

`(sleap) lab@-Mac-mini-437 ~ % pip install "sleap[nn]"
Requirement already satisfied: sleap[nn] in ./anaconda3/envs/sleap/lib/python3.13/site-packages (1.5.0)
WARNING: sleap 1.5.0 does not provide the extra 'nn'
Requirement already satisfied: attrs in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (25.4.0)
Requirement already satisfied: cattrs in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (25.3.0)
Requirement already satisfied: omegaconf in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (2.3.0)
Requirement already satisfied: imageio in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (2.37.2)
Requirement already satisfied: imageio-ffmpeg in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (0.6.0)
Requirement already satisfied: imgstore in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (0.3.7)
Requirement already satisfied: jsmin in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (3.0.1)
Requirement already satisfied: jsonpickle in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (4.1.1)
Requirement already satisfied: ndx-pose in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (0.2.2)
Requirement already satisfied: networkx in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (3.5)
Requirement already satisfied: nixio in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (1.5.4)
Requirement already satisfied: numpy in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (2.2.6)
Requirement already satisfied: opencv-python in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (4.12.0.88)
Requirement already satisfied: pandas in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (2.3.3)
Requirement already satisfied: psutil in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (7.1.3)
Requirement already satisfied: pykalman in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (0.10.2)
Requirement already satisfied: pynwb in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (3.1.2)
Requirement already satisfied: PySide6 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (6.10.0)
Requirement already satisfied: python-rapidjson in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (1.22)
Requirement already satisfied: pyyaml in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (6.0.3)
Requirement already satisfied: pyzmq in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (27.1.0)
Requirement already satisfied: qtpy in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (2.4.3)
Requirement already satisfied: rich in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (14.2.0)
Requirement already satisfied: scikit-image in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (0.25.2)
Requirement already satisfied: scikit-learn in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (1.7.2)
Requirement already satisfied: scikit-video in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (1.1.11)
Requirement already satisfied: scipy in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (1.16.3)
Requirement already satisfied: seaborn in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (0.13.2)
Requirement already satisfied: urllib3 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (2.5.0)
Requirement already satisfied: albumentations in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (2.0.8)
Requirement already satisfied: requests in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (2.32.5)
Requirement already satisfied: matplotlib in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap[nn]) (3.10.7)
Requirement already satisfied: sleap-io>=0.5.3 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap-io[all]>=0.5.3->sleap[nn]) (0.5.7)
Requirement already satisfied: h5py>=3.8.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap-io>=0.5.3->sleap-io[all]>=0.5.3->sleap[nn]) (3.15.1)
Requirement already satisfied: simplejson in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap-io>=0.5.3->sleap-io[all]>=0.5.3->sleap[nn]) (3.20.2)
Requirement already satisfied: tifffile in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap-io>=0.5.3->sleap-io[all]>=0.5.3->sleap[nn]) (2025.10.16)
Requirement already satisfied: tqdm in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap-io>=0.5.3->sleap-io[all]>=0.5.3->sleap[nn]) (4.67.1)
Requirement already satisfied: rich_click in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap-io>=0.5.3->sleap-io[all]>=0.5.3->sleap[nn]) (1.9.4)
Requirement already satisfied: hdmf>=3.13.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from ndx-pose->sleap[nn]) (4.1.1)
Requirement already satisfied: jsonschema>=3.2.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from hdmf>=3.13.0->ndx-pose->sleap[nn]) (4.25.1)
Requirement already satisfied: ruamel-yaml>=0.16 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from hdmf>=3.13.0->ndx-pose->sleap[nn]) (0.18.16)
Requirement already satisfied: jsonschema-specifications>=2023.03.6 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from jsonschema>=3.2.0->hdmf>=3.13.0->ndx-pose->sleap[nn]) (2025.9.1)
Requirement already satisfied: referencing>=0.28.4 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from jsonschema>=3.2.0->hdmf>=3.13.0->ndx-pose->sleap[nn]) (0.37.0)
Requirement already satisfied: rpds-py>=0.7.1 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from jsonschema>=3.2.0->hdmf>=3.13.0->ndx-pose->sleap[nn]) (0.28.0)
Requirement already satisfied: python-dateutil>=2.8.2 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from pandas->sleap[nn]) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from pandas->sleap[nn]) (2025.2)
Requirement already satisfied: tzdata>=2022.7 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from pandas->sleap[nn]) (2025.2)
Requirement already satisfied: platformdirs>=4.1.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from pynwb->sleap[nn]) (4.5.0)
Requirement already satisfied: six>=1.5 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from python-dateutil>=2.8.2->pandas->sleap[nn]) (1.17.0)
Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from ruamel-yaml>=0.16->hdmf>=3.13.0->ndx-pose->sleap[nn]) (0.2.14)
Requirement already satisfied: av<16.0.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap-io[all]>=0.5.3->sleap[nn]) (15.1.0)
Requirement already satisfied: pymatreader in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from sleap-io[all]>=0.5.3->sleap[nn]) (1.1.0)
Requirement already satisfied: pydantic>=2.9.2 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from albumentations->sleap[nn]) (2.12.4)
Requirement already satisfied: albucore==0.0.24 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from albumentations->sleap[nn]) (0.0.24)
Requirement already satisfied: opencv-python-headless>=4.9.0.80 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from albumentations->sleap[nn]) (4.12.0.88)
Requirement already satisfied: stringzilla>=3.10.4 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from albucore==0.0.24->albumentations->sleap[nn]) (4.2.3)
Requirement already satisfied: simsimd>=5.9.2 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from albucore==0.0.24->albumentations->sleap[nn]) (6.5.3)
Requirement already satisfied: annotated-types>=0.6.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from pydantic>=2.9.2->albumentations->sleap[nn]) (0.7.0)
Requirement already satisfied: pydantic-core==2.41.5 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from pydantic>=2.9.2->albumentations->sleap[nn]) (2.41.5)
Requirement already satisfied: typing-extensions>=4.14.1 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from pydantic>=2.9.2->albumentations->sleap[nn]) (4.15.0)
Requirement already satisfied: typing-inspection>=0.4.2 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from pydantic>=2.9.2->albumentations->sleap[nn]) (0.4.2)
Requirement already satisfied: pillow>=8.3.2 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from imageio->sleap[nn]) (12.0.0)
Requirement already satisfied: tzlocal in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from imgstore->sleap[nn]) (5.3.1)
Requirement already satisfied: contourpy>=1.0.1 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from matplotlib->sleap[nn]) (1.3.3)
Requirement already satisfied: cycler>=0.10 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from matplotlib->sleap[nn]) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from matplotlib->sleap[nn]) (4.60.1)
Requirement already satisfied: kiwisolver>=1.3.1 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from matplotlib->sleap[nn]) (1.4.9)
Requirement already satisfied: packaging>=20.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from matplotlib->sleap[nn]) (25.0)
Requirement already satisfied: pyparsing>=3 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from matplotlib->sleap[nn]) (3.2.5)
Requirement already satisfied: antlr4-python3-runtime==4.9.* in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from omegaconf->sleap[nn]) (4.9.3)
Requirement already satisfied: scikit-base<0.13.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from pykalman->sleap[nn]) (0.12.6)
Requirement already satisfied: xmltodict in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from pymatreader->sleap-io[all]>=0.5.3->sleap[nn]) (1.0.2)
Requirement already satisfied: shiboken6==6.10.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from PySide6->sleap[nn]) (6.10.0)
Requirement already satisfied: PySide6_Essentials==6.10.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from PySide6->sleap[nn]) (6.10.0)
Requirement already satisfied: PySide6_Addons==6.10.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from PySide6->sleap[nn]) (6.10.0)
Requirement already satisfied: charset_normalizer<4,>=2 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from requests->sleap[nn]) (3.4.4)
Requirement already satisfied: idna<4,>=2.5 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from requests->sleap[nn]) (3.11)
Requirement already satisfied: certifi>=2017.4.17 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from requests->sleap[nn]) (2025.10.5)
Requirement already satisfied: markdown-it-py>=2.2.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from rich->sleap[nn]) (4.0.0)
Requirement already satisfied: pygments<3.0.0,>=2.13.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from rich->sleap[nn]) (2.19.2)
Requirement already satisfied: mdurl~=0.1 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from markdown-it-py>=2.2.0->rich->sleap[nn]) (0.1.2)
Requirement already satisfied: click>=8 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from rich_click->sleap-io>=0.5.3->sleap-io[all]>=0.5.3->sleap[nn]) (8.3.0)
Requirement already satisfied: lazy-loader>=0.4 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from scikit-image->sleap[nn]) (0.4)
Requirement already satisfied: joblib>=1.2.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from scikit-learn->sleap[nn]) (1.5.2)
Requirement already satisfied: threadpoolctl>=3.1.0 in ./anaconda3/envs/sleap/lib/python3.13/site-packages (from scikit-learn->sleap[nn]) (3.6.0)
(sleap) lab@Mac-mini-437 ~ % sleap-label
Saving config: /Users/lab/.sleap/1.5.0/preferences.yaml
Restoring GUI state...

Software versions:
SLEAP: 1.5.0
Numpy: 2.2.6
Python: 3.13.5
OS: macOS-10.16-x86_64-i386-64bit-Mach-O

Happy SLEAPing! :)
2025-11-05 12:16:14.418 python3.13[79829:22256346] The class 'NSOpenPanel' overrides the method identifier.  This method is implemented by class 'NSWindow'
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No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
No module named 'sleap_nn'
Resetting monitor window.
Polling: /Users/lab/models/_251105_121624.centroid.n=174/viz/validation.*.png
Start training centroid...
Traceback (most recent call last):
  File "/Users/lab/anaconda3/envs/sleap/lib/python3.13/site-packages/sleap/gui/learning/dialog.py", line 762, in run
    new_counts = runners.run_learning_pipeline(
        labels_filename=self.labels_filename,
    ...<3 lines>...
        items_for_inference=items_for_inference,
    )
  File "/Users/lab/anaconda3/envs/sleap/lib/python3.13/site-packages/sleap/gui/learning/runners.py", line 619, in run_learning_pipeline
    trained_job_paths = run_gui_training(
        labels_filename=labels_filename,
    ...<3 lines>...
        gui=True,
    )
  File "/Users/lab/anaconda3/envs/sleap/lib/python3.13/site-packages/sleap/gui/learning/runners.py", line 751, in run_gui_training
    trained_job_path, ret = train_subprocess(
                            ~~~~~~~~~~~~~~~~^
        job_config=job,
        ^^^^^^^^^^^^^^^
    ...<3 lines>...
        waiting_callback=waiting,
        ^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/Users/lab/anaconda3/envs/sleap/lib/python3.13/site-packages/sleap/gui/learning/runners.py", line 907, in train_subprocess
    from sleap_nn.config.training_job_config import verify_training_cfg
ModuleNotFoundError: No module named 'sleap_nn'`

[talmo]

Hi @srami0619,

Unfortunately on Intel Macs you won't be able to run training (or it'll be very very slow), but at least to fix the installation issues, you can try this:

uv tool install --python 3.13 "sleap[nn]==1.5.2" --index https://download.pytorch.org/whl/cpu --index https://pypi.org/simple

Give that a go. Again, on Intel Macs you don't have the hardware to accelerate the deep learning backend, but feel free to give it a go and report back.

Cheers,

Talmo