oyLabImaging

Code for analysis and organization of microscopy data:

Install

on Linux/Mac directly from git (recommended)

conda create --name oyimg python=3.8 scipy

conda activate oyimg

if you have cuda 11.2:

pip install git+https://github.com/oylab/oyLabImaging.git#egg=oyLabImaging[cuda]

else:

pip install git+https://github.com/oylab/oyLabImaging.git#egg=oyLabImaging

add kernel to jupyter:

python -m ipykernel install --user --name=oyimg

on Linux/Mac from source:

git clone https://github.com/oylab/oyLabImaging

cd oyLabImaging

conda create --name oyimg python=3.8 scipy

conda activate oyimg

if you have cuda 11.2:

pip install -e .[cuda]

else:

pip install -e .

add kernel to jupyter:

python -m ipykernel install --user --name=oyimg

on Windows directly from git (recommended)

conda create --name oyimg python=3.8 scipy

conda activate oyimg

conda install -c conda-forge lap

if you have cuda 11.2:

pip install git+https://github.com/oylab/oyLabImaging.git#egg=oyLabImaging[cuda]

else:

pip install git+https://github.com/oylab/oyLabImaging.git#egg=oyLabImaging

add kernel to jupyter:

python -m ipykernel install --user --name=oyimg

on Windows from source:

git clone https://github.com/oylab/oyLabImaging

cd oyLabImaging

conda create --name oyimg python=3.8 scipy

conda activate oyimg

conda install -c conda-forge lap

if you have cuda 11.2:

pip install -e .[cuda]

else:

pip install -e .

add kernel to jupyter:

python -m ipykernel install --user --name=oyimg