Publications by Daniel Sage | EPFL Graph Search

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A critical role of circadian oscillators in orchestrating insulin secretion and islet gene transcription has been demonstrated recently. However, these studies focused on whole islets and did not explore the interplay between α-cell and β-cell clocks. We p ...

Combined sewer overflows and stormwater discharges represent an important source of contamination to the environment. However, the harsh environment inside sewers and particular hydraulic conditions during rain events reduce the reliability of traditional ...

An ongoing issue in vascular medicine is the measure of the blood flow. Catheterization remains the gold standard measurement method, although non-invasive techniques are an area of intense research. We hereby present a computational method for real-time m ...

We present a new method based on B-spline snakes (active contours) for measuring high-accuracy contact angles. In this approach, we avoid making physical assumptions by defining the contour of the drop as a versatile B-spline curve. When useful, we extend ...

The nematode Caenorhabditis elegans is a genetically tractable model organism to investigate sterol transport. In vivo imaging of the fluorescent sterol, dehydroergosterol (DHE), is challenged by C. elegans' high autofluorescence in the same spectral regio ...

Stem cell self-renewal, commitment and reprogramming rely on a poorly understood coordination of cell cycle progression and execution of cell fate choices. Using existing experimental paradigms, it has not been possible to probe this relationship systemati ...

The monogenic signal is the natural 2-D counterpart of the 1-D analytic signal. We propose to transpose the concept to the wavelet domain by considering a complexified version of the Riesz transform which has the remarkable property of mapping a real-value ...

Background: The yeast Schizosaccharomyces pombe is frequently used as a model for studying the cell cycle. The cells are rod-shaped and divide by medial fission. The process of cell division, or cytokinesis, is controlled by a network of signaling proteins ...

Localisation microscopy often relies on detailed models of point‐spread functions. For applications such as deconvolution or PSF engineering, accurate models for light propagation in imaging systems with a high numerical aperture are required. Different models have been proposed based on 2D Fourier transforms or 1D Bessel integrals. The most precise ones combine a vectorial description of the electric field and accurate aberration models. However, it may be unclear which model to choose as there is no compr

Discharges of combined sewer overflows (CSOs) and stormwater are recognized as an important source of environmental contamination. However, the harsh sewer environment and particular hydraulic conditions during rain events reduce the reliability of traditi ...

We give a methodology-oriented perspective on directional image analysis and rotation-invariant processing. We review the state of the art in the field and make connections with recent mathematical developments in functional analysis and wavelet theory. We unify our perspective within a common framework using operators. The intent is to provide image-processing methods that can be deployed in algorithms that analyze biomedical images with improved rotation invariance and high directional sensitivity. We sta

We propose a novel method for the clustering of point-cloud data that originate from single-molecule localization microscopy (SMLM). Our scheme has the ability to infer a hierarchical structure from the data. It takes a particular relevance when quantitati ...

Images in fluorescence microscopy are inherently blurred due to the limit of diffraction of light. The purpose of deconvolution microscopy is to compensate numerically for this degradation. Deconvolution is widely used to restore fine details of 3D biologi ...

Deconvolution is an image restoration technique which improves image contrast, resolution and signal to noise ratio. In modern optical microscopy and biological research deconvolution is becoming a fundamental processing step which allows for better image ...

We introduce a variational phase retrieval algorithm for the imaging of transparent objects. Our formalism is based on the transport-of-intensity equation (TIE), which relates the phase of an optical field to the variation of its intensity along the direct ...

Super-resolution localization microscopy methods such as PALM and STORM have been shown to provide imaging with resolutions up to a few tens of nanometers while using relatively simple setups. Biplane PALM has extended the PALM technique to three-dimension ...

We describe an approach for exploring microscopic properties of granular media that couples x-ray microtomography and distinct-element-method (DEM) simulations through image analysis. We illustrate it via the study of the intriguing phenomenon of instant a ...

The quality of super-resolution images obtained by single-molecule localization microscopy (SMLM) depends largely on the software used to detect and accurately localize point sources. In this work, we focus on the computational aspects of super-resolution ...

Background: Fluorescence loss in photobleaching (FLIP) is a widely used imaging technique, which provides information about protein dynamics in various cellular regions. In FLIP, a small cellular region is repeatedly illuminated by an intense laser pulse, ...

Accurate image annotation is essential for training artificial intelligence (AI) systems in biomedical image analysis, enabling tasks such as cell detection, tissue quantification, and disease characterization. However, creating pixel-level annotations is a time-consuming and labor-intensive process that requires expert input, limiting the development and adoption of AI methods. Recent advances in foundation models, such as the Segment Anything Model (SAM), enable interactive object segmentation from simple

Daniel Sage

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Pancreatic α- and β-Cellular Clocks Have Distinct Molecular Properties and Impact on Islet Hormone Secretion and Gene Expression

Vision-based system for the control and measurement of wastewater flow rate in sewer systems

A Feasability Study of Color Flow Doppler Vectorization for Automated Blood Flow Monitoring

A Snake-Based Approach to Accurate Determination of Both Contact Points and Contact Angles

Selective Visualization of Fluorescent Sterols in Caenorhabditis elegans by Bleach-Rate-Based Image Segmentation

Predicting stem cell fate changes by differential cell cycle progression patterns

Multiresolution Monogenic Signal Analysis Using the Riesz-Laplace Wavelet Transform

A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis

Revisiting PSF models: Unifying framework and high‐performance implementation

Flow measurements in sewer systems based on image analysis: automatic flow velocity algorithm

Transforms and Operators for Directional Bioimage Analysis: A Survey

Graphic: Graph-Based Hierarchical Clustering For Single-Molecule Localization Microscopy

DeconvolutionLab2: An Open-Source Software for Deconvolution Microscopy

Comparison of Deconvolution Software in 3D Microscopy: A User Point of View—Part 1

Variational Phase Imaging Using the Transport-of-Intensity Equation

A Psf-Based Approach To Biplane Calibration In 3D Super-Resolution Microscopy

Coupled tomography and distinct-element-method approach to exploring the granular media microstructure in a jamming hourglass

Quantitative evaluation of software packages for single-molecule localization microscopy

Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation

SAMJ: fast image annotation on ImageJ/Fiji via segment anything model