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An Open-Source Whole Slide Image Registration Workflow at Cellular Precision Using Fiji, QuPath and Elastix

Publications associées (44)

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AIDE: Accelerating image‐based ecological surveys with interactive machine learning

Devis Tuia, Benjamin Alexander Kellenberger

Ecological surveys increasingly rely on large‐scale image datasets, typically terabytes of imagery for a single survey. The ability to collect this volume of data allows surveys of unprecedented scale, at the cost of expansive volumes of photo‐interpretati ...

2020

RobustBench: a standardized adversarial robustness benchmark

Nicolas Henri Bernard Flammarion, Maksym Andriushchenko, Francesco Croce

Evaluation of adversarial robustness is often error-prone leading to overestimation of the true robustness of models. While adaptive attacks designed for a particular defense are a way out of this, there are only approximate guidelines on how to perform th ...

2020

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Visiting the Bio Imaging Search Engine (BISE) (Bio, BISE, Engine, http://biii.eu/, Imaging, Search) website at the time of writing this article, almost 1200 open source assets (components, workflows, collections) were found. This overwhelming range of offe ...

Humana Press2019

Inquiry-Based Learning with RoboGen: An Open-Source Software and Hardware Platform for Robotics and Artificial Intelligence

Dario Floreano, Joshua Evan Auerbach, Przemyslaw Mariusz Kornatowski, Alice Ghislaine Concordel

It has often been found that students appreciate hands-on work, and find that they learn more with courses that include a project than those relying solely on conventional lectures and tests. This type of project driven learning is a key component of “Inqu ...

2019

Imaging tissues and cells beyond the diffraction limit with structured illumination microscopy and Bayesian image reconstruction

Tomas Lukes, Jakub Pospisil

Background: Structured illumination microscopy (SIM) is a family of methods in optical fluorescence microscopy that can achieve both optical sectioning and super-resolution effects. SIM is a valuable method for high-resolution imaging of fixed cells or tis ...

Oxford University Press (OUP)2019

Open Source Is A-Changin': How Qualitative Research Can Help Us Adapt

In the past five years, industry has overwhelmingly turned to open source as a primary means to build products and services atop of, with around 80% of surveyed companies acknowledging that they run on open source. 66% of companies say they would first c ...

2018

Development of topological tools for the analysis of biological data

There is a growing need for unbiased clustering algorithms, ideally automated to analyze complex data sets. Topological data analysis (TDA) has been used to approach this problem. This recent field of mathematics discerns characteristic features of a space ...

EPFL2018

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In this paper we introduce an open source and reproducible microphone array hardware design and an anechoic dataset recorded with this array. The Pyramic array has 48 microphones spread onto six identical modules connected to an FPGA-ARM combo. The arrange ...

IEEE2018

Do It Yourself: From Individual Sovereignty to Civic Design

Matthew Skjonsberg

With the Usonian Automatic construction system, Frank Lloyd Wright provided citizens of Usonia—Wright’s preferred term for a culturally advanced North America—with the means of “doing it themselves,” of building their own homes and communities. Though desi ...

Museum of Modern Art - New York2017

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Inertial sensors have been employed in different types of applications in miniature embedded devices such as phones, watches, and small unmanned aerial vehicles. The stochastic structure of the error signal coming from these sensors is complex and needs to ...

2017