diSPIM preprocessing & GPU diSPIMFusion

To obtain a 3D image with isotropic resolution, diSPIM images typically require preprocessing before fusion. An ImageJ macro with a straight-forward user interface, is provided for each purpose.

Preprocessing involves background subtraction, region of interest (ROI) cropping, and 3D orientation; additionally, stage-scanning acquisitions must undergo coordinate transformation. The diSPIM Preprocessing macro performs all 4 tasks as necessary. It requires ImageJ version 1.48c or later, with Windows 7 OS.

Fusion is constituted by image registration and joint deconvolution. The GPU diSPIMFusion macro seamlessly performs both functions. It capitalizes on the GPU for parallelized computation and therefore much faster results. It requires ImageJ, Windows 7 or 10 OS, a graphics card supported by CUDA 9, and an appropriate driver for the graphics card.

Manual and code are available at GitHub.
Published at https://doi.org/10.1038/s41587-020-0560-x (preprint at bioRxiv)
Contact Min Guo at eguomin@gmail.com with questions.