23 papers · ranked by Valyu relevance
Robin Khatri, Pierre Machart, Stefan Bonn
Cell deconvolution is the estimation of cell type fractions and cell type-specific gene expression from mixed data. An unmet challenge in cell deconvolution is the scarcity of realistic training data and the domain shift often observed in synthetic training data. Here, we show that two novel deep neural networks with…
Carmen Noemí Hernández Candia, Braulio Gutiérrez-Medina, Jonathan A. Coles
'Jonathan A. Coles'] In transmitted optical microscopy, absorption structure and phase structure of the specimen determine the three-dimensional intensity distribution of the image. The elementary impulse responses of the bright field microscope therefore consist of separate absorptive and phase components, precluding…
Hayato Ikoma, Michael Broxton, Takamasa Kudo, Gordon Wetzstein
Deconvolution is widely used to improve the contrast and clarity of a 3D focal stack collected using a fluorescence microscope. But despite being extensively studied, deconvolution algorithms can introduce reconstruction artifacts when their underlying noise models or priors are violated, such as when imaging…
Peter Haub, Tobias Meckel
Colour deconvolution is a method used in diagnostic brightfield microscopy to transform colour images of multiple stained biological samples into images representing the stain concentrations. It is applied by decomposing the absorbance values of stain mixtures into absorbance values of single stains. The method assumes…
Barnali Waugh, Sharon G. Wolf, Deborah Fass, Eric Branlund + 3 more
The complex environment of biological cells and tissues has motivated development of three dimensional imaging in both light and electron microscopies. To this end, one of the primary tools in fluorescence microscopy is that of computational deconvolution. Wide-field fluorescence images are often corrupted by haze due…
Alexander Wong, Xiao Yu Wang, Maud Gorbet
Fluorescence microscopy is widely used for the study of biological specimens. Deconvolution can significantly improve the resolution and contrast of images produced using fluorescence microscopy; in particular, Bayesian-based methods have become very popular in deconvolution fluorescence microscopy. An ongoing…
Yiwei Hou, Wenyi Wang, Yunzhe Fu, Xichuan Ge + 2 more
Despite the grand advances in fluorescence microscopy, the photon budget of fluorescent molecules remains the fundamental limiting factor for major imaging parameters, such as temporal resolution, duration, contrast, and even spatial resolution. Computational methods can strategically utilize the fluorescence photons…
Zachary H. Hendrix, Peter Brown, Tim Flanagan, Douglas P. Shepherd + 2 more
Motivated Bayesian Deconvolution Authors: ['Zachary H. Hendrix' 'Peter Brown' 'Tim Flanagan' 'Douglas P. Shepherd' 'Ayush Saurabh' 'Steve Pressé'] Richardson-Lucy deconvolution is widely used to restore images from degradation caused by the broadening effects of a point spread function and corruption by photon shot…
M Laasmaa, M Vendelin, P Peterson
Although confocal microscopes have considerably smaller contribution of out-of-focus light than widefield microscopes, the confocal images can still be enhanced mathematically if the optical and data acquisition effects are accounted for. For that, several deconvolution algorithms have been proposed. As a practical…
Sylvain Prigent, Hoai-Nam Nguyen, Ludovic Leconte, Cesar Augusto Valades-Cruz + 3 more
While fluorescent microscopy imaging has become the spearhead of modern biology as it is able to generate long-term videos depicting 4D nanoscale cell behaviors, it is still limited by the optical aberrations and the photon budget available in the specimen and to some extend to photo-toxicity. A direct consequence is…
Authors not listed
4D live fluorescence microscopy is often compromised by prolonged high intensity illumination which induces photobleaching and phototoxic effects that generate photo-induced artifacts and severely impair image continuity and detail recovery. To address this challenge, we propose the CellINR framework, a case-specific…
Alexander Wong, Xiaoyu Wang, Maud Gorbet
Fluorescence microscopy is widely used for the study of biological specimens. Deconvolution can significantly improve the resolution and contrast of images produced using fluorescence microscopy; in particular, Bayesian-based methods have become very popular in deconvolution fluorescence microscopy. An ongoing…
Lena-Marie Woelk, Sukanya A. Kannabiran, Valerie Brock, Christine E. Gee + 4 more
Live cell Ca^2+^ fluorescence microscopy is a cornerstone of cellular signaling analysis and imaging. The demand for high spatial and temporal imaging resolution is, however, intrinsically linked to a low signal-to-noise ratio (SNR) of the acquired spatio-temporal image data, which impedes subsequent image analysis.…
Stephan Preibisch, Fernando Amat, Evangelia Stamataki, Mihail Sarov + 3 more
'Robert H. Singer' 'Eugene W. Myers' 'Pavel Tomančák'] Light sheet fluorescence microscopy is able to image large specimen with high resolution by imaging the samples from multiple angles. Multi-view deconvolution can significantly improve the resolution and contrast of the images, but its application has been limited…
R. Zanella, G. Zanghirati, R. Cavicchioli, L. Zanni + 3 more
'M. Bertero' 'G. Vicidomini'] Although deconvolution can improve the quality of any type of microscope, the high computational time required has so far limited its massive spreading. Here we demonstrate the ability of the scaled-gradient-projection (SGP) method to provide accelerated versions of the most used…
Boyoung Kim, Doug Brooks, Alexandra Sorvina, Shane Hickey
To investigate the cellular structure, biomedical researchers often obtain three-dimensional images by combining two-dimensional images taken along the z axis. However, these images are blurry in all directions due to diffraction limitations. This blur becomes more severe when focusing further inside the specimen as…
Imen Boujmil, Giancarlo Ruocco, Marco Leonetti
Super resolution techniques are an excellent alternative to wide field microscopy, providing high resolution also in (typically fragile) biological sample. Among the various super resolution techniques, Structured Illumination Microscopy (SIM) improve resolution by employing multiple illumination patterns to be…
Haohong Gan, Shiyi Peng, Hailian Hu, Xuan You + 4 more
The resolving power of optical microscopy is fundamentally constrained by the diffraction of light, limiting our ability to visualize subcellular structures. Computational methods, particularly deconvolution, can restore blurred images but critically depend on an accurate point spread function (PSF), whose estimation…
Alon Tchelet, Leonardo Mussa, Stefano Vojinovic
Cornea cell count is an important diagnostic tool commonly used by practitioners to assess the health of a patient's cornea. Unfortunately, clinical specular microscopy requires the acquisition of a large number of images at different focus depths because the curved shape of the cornea makes it impossible to acquire a…
Authors not listed
Electrochemical impedance spectroscopy (EIS) coupled with distribution of relaxation times (DRT) analysis is a robust framework for characterizing electrochemical systems. However, DRT deconvolution is often plagued by spurious peaks, hindering accurate process identification and quantitative parameter estimation. To…
Adeleke Maradesa, Baptiste Py, Ting Hei Wan, Mohammed B. Effat + 1 more
Electrochemical impedance spectroscopy (EIS) is a characterization technique used widely in electrochemistry. Obtaining EIS data is simple when modern electrochemical workstations are used; however, analyzing EIS spectra is still a considerable quandary. The distribution of relaxation times (DRT) has emerged as a…
Emanuele Quattrocchi, Baptiste Py, Adeleke Maradesa, Quentin Meyer + 2 more
Electrochemical impedance spectroscopy (EIS) is a characterization technique widely used to evaluate the properties of electrochemical systems. The distribution of relaxation times (DRT) has emerged as a model-free alternative to equivalent circuits and physical models to circumvent the inherent challenges of EIS…
Authors not listed
Vertex models have been established as powerful tools for the cell-based simulation of epithelial tissues as they allow a detailed description of their mechanical development with respect to the properties of individual cells. Thus, they suit the challenges of simulating intestinal organoids which arise from the…