Publications by Daniel Sage | EPFL Graph Search

Surpassing light inhomogeneities in structured-illumination microscopy with FlexSIM

Super-resolution structured-illumination microscopy (SIM) is a powerful technique that allows one to surpass the diffraction limit by up to a factor two. Yet, its practical use is hampered by its sensitivity to imaging conditions which makes it prone to re ...

2024

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

Daniel Sage

Nature Portfolio2024

Back to the future–20 years of progress and developments in photonic microscopy and biological imaging

Daniel Sage

In 2023, the ImaBio consortium (imabio-cnrs.fr), an interdisciplinary life microscopy research group at the Centre National de la Recherche Scientifique, celebrated its 20th anniversary. ImaBio contributes to the biological imaging community through organi ...

2024

A framework for evaluating the performance of SMLM cluster analysis algorithms

Daniel Sage, Juliette Griffie

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. ...

NATURE PORTFOLIO2023

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

Daniel Sage, Virginie Sophie Uhlmann, Laurène Donati

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 ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2022

Steer'n'Detect: fast 2D template detection with accurate orientation estimation

Michaël Unser, Daniel Sage, Zsuzsanna Püspöki, Julien René Pierre Fageot

Motivation: Rotated template matching is an efficient and versatile algorithm to analyze microscopy images, as it automates the detection of stereotypical structures, such as organelles that can appear at any orientation. Its performance however quickly de ...

2022

Correction of multiple-blinking artifacts in photoactivated localization microscopy

Daniel Sage, Juliette Griffie

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 ...

NATURE PORTFOLIO2022

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

Michaël Unser, Daniel Sage, Olivier Burri, Cathrin Brisken, Quentin Juppet, Fabio De Martino, Martin Weigert

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 ...

2021

Optimal-Transport-Based Metric for SMLM

Michaël Unser, Daniel Sage, Thanh-An Michel Pham, Quentin Alain Denoyelle, Pol del Aguila Pla

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 ...

IEEE2021

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

Michaël Unser, Daniel Sage, Shayan Aziznejad

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 ...

IEEE2021

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

Michaël Unser, Daniel Sage, Laurène Donati

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. ...

NATURE PORTFOLIO2021

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

Daniel Sage

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 ...

National Academy of Sciences2020

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

Daniel Sage, Sabine Süsstrunk, Thierry Laroche, Arne Seitz, Ruofan Zhou, Majed El Helou

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 ...

2020

Achieving high-resolution thermal imagery in low-contrast lake surface waters by aerial remote sensing and image registration

Ulrich Lemmin, Daniel Sage, David Andrew Barry, Abolfazl Irani Rahaghi

A two-platform measurement system for realizing airborne thermography of the Lake Surface Water Temperature (LSWT) with ~0.8 m pixel resolution (sub-pixel satellite scale) is presented. It consists of a tethered Balloon Launched Imaging and Monitoring Plat ...

2019

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

Michaël Unser, Daniel Sage, Ricardo Henriques, Thanh-An Michel Pham, Thomas Pengo, Seamus John Holden, Tomas Lukes, Anna Archetti, Silvia Colabrese, Anurag Agrawal

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 ...

2019

Deforming Tessellations for the Segmentation of Cell Aggregates

Michaël Unser, Daniel Sage, Aymeric Alexandre Galan, Anaïs Laure Marie-Thérèse Badoual

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 ...

IEEE2019

Closed-Form Expression of the Fourier Ring-Correlation for Single-Molecule Localization Microscopy

Michaël Unser, Daniel Sage, Thanh-An Michel Pham, Emmanuel Emilien Louis Soubies

Single-molecule localization microscopy (SMLM) is a popular microscopic technique that achieves super resolution imaging by localizing individual blinking molecules in thousands of frames. Therefore, the reconstructed high-resolution image is a combination ...

IEEE2019

Pocket guide to solve inverse problems with GlobalBioIm

Michaël Unser, Daniel Sage, Laurène Donati, Thanh-An Michel Pham, Ferréol Arnaud Marie Soulez, Michael Thompson McCann, Emmanuel Emilien Louis Soubies, Thomas Jean Debarre

GlobalBioIm is an open-source MATLAB (R) library for solving inverse problems. The library capitalizes on the strong commonalities between forward models to standardize the resolution of a wide range of imaging inverse problems. Endowed with an operator-al ...

2019

Parametric Experimental Study and Design of Experiment Modelling of Sapphire Grinding

Daniel Sage

This study investigates and models the grinding process of single crystal sapphire. Five parameters: the wheel speed, the feed speed, the vertical feed, the ultrasonic assistance and the crystallographic direction were considered via a design of experiment ...

Elsevier2017

Investigating Focal Adhesion Substructures by Localization Microscopy

Daniel Sage, Aleksandra Radenovic, Lely Feletti, Hendrik Georges Deschout

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 ...

Elsevier2017