General package requirements


If you encounter issues related to lap and numpy, please install numpy first and then install lap. If there are any issues with numba and numpy, please follow the error messages and resolve numba and numpy version issues.

Install dependencies by running:

pip install -r requirements.txt
pip install -r napari_requirements.txt
pip install lap[alldeps]
pip install .

Alternatively, to install an editable version and develop the package, run:

pip install -e .

Pytorch (including torchvision)

Please refer to the Pytorch Official Website for the most recent installation instructions. Here we simply provide two examples used in our cases.

Install via conda:

conda install pytorch torchvision -c pytorch

An example on 2080Ti/3090 workstations with CUDA 11.7, run:

conda install pytorch torchvision torchaudio pytorch-cuda=11.7 -c pytorch -c nvidia

Check if you are using cuda (refer to PyTorch docs for TPU or other devices) using the commands torch.cuda.is_available(), torch.cuda.current_device(), and torch.cuda.device_count().

Detectron2 (optional)

Please refer to the latest detectron2 documentation to install detectron2 for segmentation if you cannot build from source with the following commands.

Prebuilt (Easier and preferred by us) can be found detectron2 install documentation.

Or, you can build from source by following the instructions detectron2 build documentation. For building from source option, run:

git clone
python -m pip install -e detectron2

For {avi, mp4} movie generation functionality provided by livecellx, run:

conda install -c conda-forge ffmpeg

Precommit [Dev]

To install pre-commit, run:

pip install pre-commit
pre-commit install