Publications de Daniel Sage | EPFL Graph Search

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We propose the use of Flat Metric to assess the performance of reconstruction methods for single-molecule localization microscopy (SMLM) in scenarios where the ground-truth is available. Flat Metric is intimately related to the concept of optimal transport ...

Dehydroergosterol (DHE) is an intrinsically fluorescent sterol with absorption/emission in the ultraviolet (UV) region and biophysical properties similar to those of cholesterol. We compared the potential of UV-sensitive low-light-level wide-field (UV-WF) ...

This chapter describes tools and techniques that facilitate a gentle introduction to fascinating concepts in digital image processing from four leading universities. Equipped with informative visualizations and a user-friendly interfaces, these modules are currently being used effectively in a classroom environment for teaching DIP at many universities across the world.

Patient-Derived Xenografts (PDXs) are the preclinical models which best recapitulate inter- and intra-patient complexity of human breast malignancies, and are also emerging as useful tools to study the normal breast epithelium. However, data analysis gener ...

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 ...

Following on from the emerging importance of the pancreas circadian clock on islet function and the development of type 2 diabetes in rodent models, we aimed to examine circadian gene expression in human islets. The oscillator properties were assessed in i ...

This analysis compares the performance of seven algorithms for cluster analysis of single-molecule localization microscopy data. The results provide a framework for comparing these types of methods and point users to the best tools. ...

Mammalian circadian oscillators are considered to rely on transcription/translation feedback loops in clock gene expression. The major and essential loop involves the autorepression of cryptochrome (Cry1, Cry2) and period (Per1, Per2) genes. The rhythm-gen ...

We present a new active contour to segment cell aggregates. We describe it by a smooth tessellation that is attracted toward the cell membranes. Our approach relies on subdivision schemes that are tightly linked to the theory of wavelets. The shape is enco ...

Edge-preserving smoothers need not be taxed by a severe computational cost. We present, in this paper, a lean algorithm that is inspired by the bi-exponential filter and preserves its structure-a pair of one-tap recursions. By a careful but simple local ad ...

Background: Fluorescent and bioluminescent time-lapse microscopy approaches have been successfully used to investigate molecular mechanisms underlying the mammalian circadian oscillator at the single cell level. However, most of the available software and ...

Photoactivated localization microscopy (PALM) produces an array of localization coordinates by means of photoactivatable fluorescent proteins. However, observations are subject to fluorophore multiple blinking and each protein is included in the dataset an ...

With the widespread uptake of two-dimensional (2D) and three-dimensional (3D) single-molecule localization microscopy (SMLM), a large set of different data analysis packages have been developed to generate super-resolution images. In a large community effo ...

A 2016 competition to find the optimum software for 3D single-molecule localization microscopy will help practitioners choose the best tool for the job and spur further developments in the field. ...

DeepImageJ offers a user-friendly solution in ImageJ to run trained deep learning models for biomedical image analysis. It includes guiding tools for reliable analyses, contributing to the democratization of deep learning in microscopy. ...

Elucidation of in vivo cholesterol transport and its aberrations in cardiovascular diseases requires suitable model organisms and the development of appropriate monitoring technology. We recently presented a new approach to visualize transport of the intri ...

Daniel Sage

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Optimal-Transport-Based Metric for SMLM

Potential of Ultraviolet Wide-Field Imaging and Multiphoton Microscopy for Analysis of Dehydroergosterol in Cellular Membranes

Image Processing Education

Deep Learning Enables Individual Xenograft Cell Classification in Histological Images by Analysis of Contextual Features

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

Autonomous and self-sustained circadian oscillators displayed in human islet cells

Vision-Based System for the Control and Measurement of Wastewater Flow Rate in Sewer Systems

A framework for evaluating the performance of SMLM cluster analysis algorithms

Circadian gene expression is resilient to large fluctuations in overall transcription rates

Deforming Tessellations for the Segmentation of Cell Aggregates

Bi-Exponential Edge-Preserving Smoother

A software solution for recording circadian oscillator features in time-lapse live cell microscopy

Correction of multiple-blinking artifacts in photoactivated localization microscopy

Effect of Ageing on Elastin Functionality in Human Cerebral Arteries

Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software

Super-Resolution Fight Club

JDLL: a library to run deep learning models on Java bioimage informatics platforms

DeepImageJ: A user-friendly environment to run deep learning models in ImageJ

Selective visualization of fluorescent sterols in Caenorhabditis elegans

Multicolor Bleach-Rate Imaging Enlightens in vivo Sterol Transport