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spots3d

GPU accelerated spot finding and localization for both skewed (diSPIM, lattice, OPM) and standard geometry (widefield, confocal) 3D microscopy data.

Install

Create a python>=3.10 and CUDA >=11.2, <12.0 environment. We will use conda (or mamba if you prefer) for the CUDA and CuPy installation.

For Linux OS:

conda create -n spots3d python=3.10
conda activate spots3d
conda install -c conda-forge -c rapidsai -c nvidia cudatoolkit=11.8 cupy cucim=24.02 cuda-version=11.8 cudnn cutensor

For Windows OS:

conda create -n spots3d python=3.10
conda activate spots3d
conda install -c conda-forge -c nvidia cudatoolkit=11.8 cupy cuda-version=11.8 cudnn cutensor

On Windows OS, the required skimage portion of cuCIM will be built and installed during spots3d installation.

Then, build and install the qi2lab branch of Gpufit.

Finally, install spots3d

pip install spots3d@git+https://[email protected]/qi2lab/spots3d@main#egg=spots3d

An optional, but recommended napari plugin for spot localization, that uses SPOTS3D and the qi2lab branch of Gpufit, is found at napari-spot-detection.