Publications de Daniel Sage | EPFL Graph Search

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Since the pioneering work of Hirschfeld, it is known that time-integrated emission (TiEm) of a fluorophore is independent of fluorescence quantum yield and illumination intensity. Practical implementation of this important result for determining exact prob ...

The Schizosaccharomyces pombe septation initiation network (SIN) regulates cytokinesis, and asymmetric association of SIN proteins with the mitotic spindle pole bodies (SPBs) is important for its regulation. Here, we have used semi-automated image analysis ...

Circadian clocks operative in pancreatic islets participate in the regulation of insulin secretion in humans and, if compromised, in the development of type 2 diabetes (T2D) in rodents. Here we demonstrate that human islet alpha- and beta-cells that bear a ...

This chapter addresses the main aspects of computational bioimaging applied to the microscopy of living organisms. It explains the current context of microscopy imaging, and presents the most notable operations of image processing and image analysis of microscopy under the dual umbrella of model-based and data-driven approaches. The chapter provides the general principles underlying algorithms and the terms used in the field allowing for more in-depth research. Image formation in fluorescence microscopy fol

In fluorescence microscopy live-cell imaging, there is a critical trade-off between the signal-to-noise ratio and spatial resolution on one side, and the integrity of the biological sample on the other side. To obtain clean high-resolution (HR) images, one ...

The variety of bioimage data and their quality have dramatically increased over the last decade. In parallel, the number of proposed deep learning (DL) models for their analysis grows by the day. Yet, the adequate reuse of published tools by practitioners ...

We present a new, robust algorithm for tracking fluorescent particles in dynamic image sequences obtained by brightfield or confocal microscopy. Specifically, we consider the problem of extracting the movement of chromosomal telomeres within the nucleus of a budding yeast cell. Our method has three components. The first is an alignment module that compensates for the movement of the biological structure under investigation. In our application, the images are aligned to the center of gravity of the nucleus w

Localization microscopy relies on computationally efficient Gaussian approximations of the point spread function for the calculation of fluorophore positions. Theoretical predictions show that under specific experimental conditions, localization accuracy i ...

Fluorescence resonance energy transfer (FRET) allows the user to investigate interactions between fluorescent partners. One crucial issue when calculating sensitized emission FRET is the correction for spectral bleed-throughs (SBTs), which requires to calc ...

Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning (ML) are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap encompasses key aspects of how ML is applied to microscopy image data, with the a

We present a unifying framework for point-spread function (PSF) models in high-numerical-aperture optical microscopy. Starting from the Richards-Wolf integral, we demonstrate the mathematical equivalence between Fourier-based and Bessel-based approaches as alternative parameterizations of the same propagation integral. This framework enables us to generalize correction factors such as Gibson-Lanni aberrations, apodisation, and arbitrary phase masks to both scalar and vectorial models. We provide an open-sou

Image processing (IP) can be taught very effectively by complementing the basic lectures with computer laboratories where the participants can actively manipulate and process images. This offering can be made even more attractive by allowing the students to develop their own IP code within a reasonable time frame. After a brief review of existing software packages that can be used for teaching IP, we present a system that we have designed to be as “student-friendly” as possible. The software is built around

Motivation: SpotCaliper is a novel wavelet-based image-analysis software providing a fast automatic detection scheme for circular patterns (spots), combined with the precise estimation of their size. It is implemented as an ImageJ plugin with a friendly us ...

Phosphorylation is involved in numerous neurodegenerative diseases. In particular, alpha-synuclein is extensively phosphorylated in aggregates in patients suffering from synucleinopathies. However, the share of this modification in the events that lead to ...

Deconvolution is an image processing technique that restores the effective object representation [3] [4], allowing to improve images analysis steps such as segmentation [1] or colocalization study [2]. We performed several deconvolution tests on different ...

Context: The circadian clock represents the body's molecular time-keeping system. Recent findings revealed strong changes of clock gene expression in various types of human cancers. Objective: Due to emerging evidence on the connection between the circadia ...

It is well known that spatial averaging can be realized (in space or frequency domain) using algorithms whose complexity does not scale with the size or shape of the filter. These fast algorithms are generally referred to as constant-time or O(1) algorithm ...

This contribution presents a simple, fast, and low-cost method to track in situ and in real time the evolution of the surface topography. The method combines an optical method (collimated light) with image analysis. The method was validated using a complex ...

Cells rely on focal adhesions (FAs) to carry out a variety of important tasks, including motion, environmental sensing, and adhesion to the extracellular matrix. Although attaining a fundamental characterization of FAs is a compelling goal, their extensive ...

As the field of bioimage informatics matures, the issue of the validation of image reconstruction algorithms and the definition of proper performance criteria becomes more pressing. In this work, we discuss benchmarking aspects of fluorescence microscopy q ...

Daniel Sage

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Photobleaching Kinetics and Time-Integrated Emission of Fluorescent Probes in Cellular Membranes

Analysis of S. pombe SIN protein association to the SPB reveals two genetically separable states of the SIN

In pancreatic islets from type 2 diabetes patients, the dampened circadian oscillators lead to reduced insulin and glucagon exocytosis

Image Processing and Image Analysis in Microscopy

W2S: Microscopy Data with Joint Denoising and Super-Resolution for Widefield to SIM Mapping

A Practical Guide to Supervised Deep Learning for Bioimage Analysis: Challenges and good practices

Automatic Tracking of Particles in Dynamic Fluorescence Microscopy

3-D PSF fitting for fluorescence microscopy: implementation and localization application

PixFRET, an ImageJ Plug-in for FRET Calculation That Can Accommodate Variations in Spectral Bleed-throughs

Roadmap on Deep Learning for Microscopy

Revisiting PSF models: theory and implementation

Teaching Image-Processing Programming in Java

SpotCaliper: Fast Wavelet-Based Spot Detection with Accurate Size Estimation

Phosphorylation does not prompt, nor prevent, the formation of alpha-synuclein toxic species in a rat model of Parkinson's disease

Comparison of Deconvolution Software: A User Point of View—Part 2

Circadian Clock Characteristics Are Altered in Human Thyroid Malignant Nodules

Fast O(1) Bilateral Filtering Using Trigonometric Range Kernels

A Simple, Fast and Low-Cost Method for in situ Monitoring of Topographical Changes and Wear Rate of a Complex Tribo-System Under Mixed Lubrication

Investigating Focal Adhesion Substructures by Localization Microscopy

Benchmarking Image-Processing Algorithms for Biomicroscopy: Reference Datasets and Perspectives