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Oblique plane microscopy, OPM, is a form of lightsheet microscopy that permits volumetric imaging of biological samples at high temporal and spatial resolution. However, the imaging geometry of OPM, and related variants of light sheet…
We present a novel learning-based method to build a differentiable computational model of a real fluorescence microscope. Our model can be used to calibrate a real optical setup directly from data samples and to engineer point spread…
This paper proposes a non-computational method of counteracting the effect of image degradation introduced by the diffraction phenomenon in lensless microscopy. All the optical images (whether focused by lenses or not) are diffraction…
Light sheet microscopy promises to revolutionize developmental biology by enabling live in toto imaging of entire embryos with minimal phototoxicity. We present detailed instructions for building a compact and customizable Selective Plane…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…
SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule…
Image simulation remains under-exploited for the most widely used biological phase microscopy methods, because of difficulties in simulating partially coherent illumination. We describe an open-source toolbox, microlith…
Light microscopy is a widespread and inexpensive imaging technique facilitating biomedical discovery and diagnostics. However, light diffraction barrier and imperfections in optics limit the level of detail of the acquired images. The…
This paper presents a generic framework for the numerical simulation of transformation-diffusion processes in complex volume geometric shapes. This work follows a previous one devoted to the simulation of microbial degradation of organic…
Imaging biological molecules in the gas-phase requires novel sample delivery methods, which generally have to be characterized and optimized to produce high-density particle beams. A non-destructive characterization method of the transverse…
Background: Photoacoustic Microscopy (PAM) integrates optical and acoustic imaging, offering enhanced penetration depth for detecting optical-absorbing components in tissues. Nonetheless, challenges arise in scanning large areas with high…
We present the 'simage' software suite for the simulation of artificial extragalactic images, based empirically around real observations of the Hubble Ultra Deep Field (UDF). The simulations reproduce galaxies with realistic and complex…
Light-sheet fluorescence microscopy (LSFM) is used to capture volume images of biological specimens. It offers high contrast deep inside densely fluorescence labelled samples, fast acquisition speed and minimal harmful effects on the…
The focus of this paper is the numerical solution of a pore-scale model for the growth of a permeable biofilm. The model includes water flux inside the biofilm, different biofilm components, and shear stress on the biofilm-water interface.…
Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…
We developed a Bessel-beam photoacoustic microscopical simulation platform by using the k-Wave: MATLAB toolbox. The simulation platform uses the ring slit method to generate Bessel beam. By controlling the inner and outer radius of the ring…
Scanning Transmission Electron Microscopy (STEM) is a critical tool for imaging the properties of materials and biological specimens at atomic scale, yet our understanding of relevant electron beam damage mechanisms is incomplete. Recent…
Realistic simulations of experiments at large scale photon facilities, such as optical laser laboratories, synchrotrons, and free electron lasers, are of vital importance for the successful preparation, execution, and analysis of these…
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we observed a dramatic increase…
Simulated images are essential in algorithm development and instrument testing for optical telescopes. During real observations, images obtained by optical telescopes are affected by spatially variable point spread functions (PSFs), a…