Dependencies

Before installing the rest of the dependencies make sure you are in the new devbio-napari based environment you created in the last section. Type the following.

mamba activate decon-dl-env

Cuda and Cupy

Note: You can probably use a version different than 11, just make sure cudatookkit and cupy versions are compatible.

mamba install -c conda-forge cudatoolkit=11.2 cudnn=8.1.0
pip install cupy-cuda11x

tnia-python and clij2-fft

The tnia-python library is used for projections and some helper functions, clij2-fft is used for deconvolution, and psfmodels is used for diffractions based PSFs.

pip install tnia-python
pip install clij2-fft
pip install psfmodels

Stardist and CSB Deep

These libraries are used for deep learning and require Tensorflow. For Windows we need to install tensorflow<2.11. The tensorflow version (<2.11) is not required for Mac or Linux.

pip install "tensorflow<2.11"

Then install stardist which should also install CSBDeep

pip install stardist

Cellpose

pip install "opencv-python-headless<4.3"
pip install cellpose

raster-geometry

Raster-Geometry is used to generate simulate images for deconvolution testing and deep learning training.

pip install raster-geometry

Additional for Mac and Linux users

Mac-users may also need to install this:

conda install -c conda-forge ocl_icd_wrapper_apple

Linux users may also need to install this:

conda install -c conda-forge ocl-icd-system