napari-spot-detection

Interactive parameters selection and visualization of intermediate results for spot detection.

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This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

You can install napari-spot-detection via pip: pip install napari-spot-detection For now the package has complex dependencies, hence the lack of automated tests and CI.
You'll need ideally a working CUDA installation (brace yourself), and non optionally, the custom versions of GPUfit as well as the localize-psf library:

# Prepare installation directory
INSTALL_DIR='~/Programs'  # where libraries will be downloaded and installed
mkdir -p $INSTALL_DIR
cd $INSTALL_DIR

# activate your pyenv of conda python environment, then:

# Install GPUfit:
git clone https://github.com/QI2lab/Gpufit.git
cd Gpufit
# path to cmake command
cmake_path=$(which cmake)
# directory where gpu
build_dir="../gpufit_build"
mkdir $build_dir
cd $build_dir
$cmake_path -DCMAKE_BUILD_TYPE=RELEASE ../Gpufit
make
# go to the folder with compiled library pyGpufit
cd $build_dir/pyGpufit
pip install .

cd $INSTALL_DIR
# Install localize-psf:
git clone https://github.com/QI2lab/localize-psf.git
cd localize-psf
# in setup.py I changed `extras = {'gpu': ['cupy'],` to `extras = {'gpu': ['cupy-cuda114'],`
# to match my CUDA installation and avoid a ore recent (incompatible) version to be installed
pip install --no-cache-dir .['gpu']
# or pip install --no-cache-dir . if CUDA is not available

# Install napari-spot-detection:
cd $INSTALL_DIR
git clone https://github.com/AlexCoul/napari-spot-detection.git
cd napari-spot-detection
pip install .
# or pip install -e .  if you want to modify the plugin

To install latest development version :

pip install git+https://github.com/AlexCoul/napari-spot-detection.git

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the GNU GPL v3.0 license, "napari-spot-detection" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.