SPITFIR(e) software: SParse fIT for Fluorescence Image Restoration



SPITFIR(e) (SParse fIT for Fluorescence Image Restoration) is a very flexible software designed to restore 2D-3D+Time fluorescent images and subtract undesirable out-of-focus background. We assume that the images are sparse and piece-wise smooth, and are corrupted by mixed Poisson-Gaussian noise. The principle resides in the minimization of a convex energy functional that includes a fidelity-to-data termand a Sparse-Hessian Variation regularization term. A fast primal-dual optimization algorithm allows to restore very large images in a few seconds. SPITFIR(e) is nearly parameter-free as the practitioner needs only to specify the amount of desired sparsity (weak, moderate, high). Experimental results in lattice light sheet, stimulated emission depletion, multifocus microscopy, spinning disk confocal, and wide-field microscopy demonstrate the generic ability of the SPITFIR(e) algorithmto efficiently reduce noise and blur, and to subtract undesirable fluorescent background, while avoiding the emergence of deconvolution artifacts.

Software distribution

SPITFIR(e) algorithm has been implemented both in CPU and GPU, is interfaced with Napari (https://www.napari-hub.org/plugins/napari-sdeconv) and can be downloaded for free here: https://github.com/sylvainprigent/simglib.


S. Prigent, H.-N. Nguyen, L. Leconte, C. A. Valades-Cruz, B. Hajj, J. Salamero and C. Kervrann. SPITFIRe: a supermaneuverable algorithm for restoring 2D-3D fluorescence images and videos,  and background subtraction, bioRxiv-2022.01.04.474883HAL-INRIA-03518618, 2022

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