Simultaneous recovery of both bright and dim structures from noisy fluorescence microscopy images using a modified TV constraint

Abstract

Summary The quality and information content of biological images can be significantly enhanced by postacquisition processing using deconvolution and denoising. However, when imaging complex biological samples, such as neurons, stained with fluorescence labels, the signal level of different structures can differ by several orders of magnitude. This poses a challenge as current image reconstruction algorithms are focused on recovering low signals and generally have sample‐dependent performance, requiring tedious manual tuning. This is one of the main hurdles for their wide adoption by nonspecialists. In this work, we modify the general constrained reconstruction method (in our case utilizing a total variation constraint) so that both bright and dim structures can drive the deconvolution with equal force. In this way, we can simultaneously obtain high‐quality reconstruction across a wide range of signals within a single image or image sequence. The algorithm is tested on both simulated and experimental data. When compared with current state‐of‐art algorithms, our algorithm outperforms others in terms of maintaining the resolution in the high‐signal areas and reducing artefacts in the low‐signal areas. The algorithm was also tested on image sequences where one set of parameters are used to reconstruct all images, with blind evaluation by a group of biologists demonstrating a marked preference for the images produced by our method. This means that our method is suitable for batch processing of image sequences obtained from either spatial or temporal scanning. Lay Description Fluorescence microscopy images of complex biological samples contain a wide range of signal levels. This signal variation leads current reconstruction algorithms, which aim to enhance the quality of the raw images, to have sample‐dependent performance. In this work, we design a new optimization that allows the reconstruction to “pay equal eqattention to” both bright and dim structures. In this way, we can simultaneously recover both bright and dim structures within a single image or image sequence, as validated when the algorithm was quantitatively tested on both simulated and experimental data. When our method was evaluated alongside current state of art algorithms by a group of biologists, our algorithm was considered qualitatively superior.

Supplementary document for Simultaneous 3D deconvolution and halo removal for spatial light interference microscopy through a two-edge-apodized wiener filter - 5619802.pdf

“…However, it still suffered from artifacts in the case of dim structure, such as endoplasmic reticulum (ER). To reduce such artifacts, we used total variation(TV) [5,6] constraint to suppress the noise while In order to speed up the convergence, we have used the split Bregman method [7] to solve the problem shown in Eq. S1.We assume that w is an approximation of ∇v, and the optimization Eq.…”