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, Laurène Donati, Virginie Sophie Uhlmann

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, Cathrin Brisken, Daniel Sage, Olivier Burri, 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