RedLionfish – fast Richardson-Lucy Deconvolution package for efficient point spread function suppression in volumetric data [version 1; peer review: 2 approved]

Abstract

The experimental limitations with optics observed in many microscopy and astronomy instruments result in detrimental effects for the imaging of objects. This can be generally described mathematically as a convolution of the real object image with the point spread function that characterizes the optical system. The popular Richardson-Lucy (RL) deconvolution algorithm is widely used for the inverse process of restoring the data without these optical aberrations, often a critical step in data processing of experimental data. Here we present the versatile RedLionfish python package, that was written to make the RL deconvolution of volumetric (3D) data easier to run, very fast (by exploiting GPU computing capabilities) and with automatic handling of hardware limitations for large datasets. It can be used programmatically in Python/numpy using conda or PyPi package managers, or with a graphical user interface as a napari plugin.

Keywords

• Python
• Image processing
• Microscopy
• napari
• Fluorescence Light Microscopy
• Correlative imaging
• eng