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Fast Parametric Snakes For 3D Microscopy

Related publications (32)

Compact and effective photon-resolved image scanning microscope

Fluorescence confocal laser-scanning microscopy (LSM) is one of the most popular tools for life science research. This popularity is expected to grow thanks to single-photon array detectors tailored for LSM. These detectors offer unique single-photon spati ...

Spie-Soc Photo-Optical Instrumentation Engineers2024

Material removing tool and method for designing the same

Jean-François Molinari, Son-Jonathan Pham-Ba

The invention relates to a material removing tool, such as an ice cream scoop, and method for designing the same. The material removing tool has a shape optimized to minimize the amount of work the user has to provide in order to form and remove a piece of ...

2022

Weakly Supervised Deep Learning Methods for Biomicroscopy

Adrian Shajkofci

Optical microscopy, an invaluable tool in biology and medicine to observe and quantify cellular function, organ development, or disease mechanisms, requires constant trade-offs between spatial, temporal, and spectral resolution, invasiveness, acquisition t ...

EPFL2021

Spatially-Variant CNN-Based Point Spread Function Estimation for Blind Deconvolution and Depth Estimation in Optical Microscopy

Michael Stefan Daniel Liebling, Adrian Shajkofci

Optical microscopy is an essential tool in biology and medicine. Imaging thin, yet non-flat objects in a single shot (without relying on more sophisticated sectioning setups) remains challenging as the shallow depth of field that comes with high-resolution ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2020

Development of novel experimental and computational methods for three-dimensional coherent and super-resolution microscopy

Adrien Charles-François Raymond Descloux

Optical microscopy is one widely used tool to study cell functions and the interaction of molecules at a sub-cellular level. Optical microscopy techniques can be broadly divided into two categories: partially coherent and incoherent. Coherent microscopy te ...

EPFL2020

Software Tools for Handling Magnetically Collected Ultra-thin Sections for Microscopy

Jelena Banjac

This report presents the software tools that will be available online to help users accurately segment ultra-thin sections of brain tissue in a large image to determine the section’s coordinates. In order to predict these coordinates, the goal was to use a ...

2019

Virtual High-Framerate Microscopy of the Beating Heart via Sorting of Still Images

Michael Stefan Daniel Liebling, Olivia Mariani

Microscopy of the beating heart in embryos provides key insights for the study of its development. However, achieving a sufficiently high framerate is difficult with conventional cameras. Here, we present a method to reconstruct an image sequence covering ...

Idiap2019

Mean-Field methods for Structured Deep-Learning in Computer Vision

Pierre Bruno Baqué

In recent years, Machine Learning based Computer Vision techniques made impressive progress. These algorithms proved particularly efficient for image classification or detection of isolated objects. From a probabilistic perspective, these methods can predi ...

EPFL2018

Semi-Blind Spatially-Variant Deconvolution in Optical Microscopy with Local Point Spread Function Estimation By Use Of Convolutional Neural Networks

Michael Stefan Daniel Liebling, Adrian Shajkofci

We present a semi-blind, spatially-variant deconvolution technique aimed at optical microscopy that combines a local estimation step of the point spread function (PSF) and deconvolution using a spatially variant, regularized Richardson-Lucy algorithm. To f ...

2018

DeconvolutionLab2: An Open-Source Software for Deconvolution Microscopy

Michaël Unser, Daniel Sage, Laurène Donati, Cédric René Jean Vonesch, Ferréol Arnaud Marie Soulez, Denis Fortun, Guillaume Schmit

Images in fluorescence microscopy are inherently blurred due to the limit of diffraction of light. The purpose of deconvolution microscopy is to compensate numerically for this degradation. Deconvolution is widely used to restore fine details of 3D biologi ...

2017

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