Publications by Michael Stefan Daniel Liebling

From Nano to Macro An overview of the IEEE Bio Image and Signal Processing Technical Committee

Michael Stefan Daniel Liebling, Michaël Unser, Dimitri Nestor Alice Van De Ville

The Bio Image and Signal Processing (BISP) Technical Committee (TC) of the IEEE Signal Processing Society (SPS) promotes activities within the broad technical field of biomedical image and signal processing. Areas of interest include medical and biological ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2023

Estimating Nonplanar Flow from 2D Motion-blurred Widefield Microscopy Images via Deep Learning

Michael Stefan Daniel Liebling, Adrian Shajkofci

Optical flow is a method aimed at predicting the movement velocity of any pixel in the image and is used in medicine and biology to estimate flow of particles in organs or organelles. However, a precise optical flow measurement requires images taken at hig ...

IEEE2021

Perspectives and limitations of visible-thermal image pair synthesis via generative adversarial networks

Michael Stefan Daniel Liebling, François Thierry M Marelli

Many applications rely on thermal imagers to complement or replace visible light sensors in difficult imaging conditions. Recent advances in machine learning have opened the possibility of analyzing or enhancing images, yet these methods require large anno ...

SPIE-INT SOC OPTICAL ENGINEERING2021

Optics Versus Computation: Influence of Illumination and Reconstruction Model Accuracy in Focal-Plane-Scanning Optical Projection Tomography

Michael Stefan Daniel Liebling

Optical Projection Tomography (OPT) imaging provides isotropic resolution for samples up to a few millimeters. High resolution OPT is achieved by deconvolving Focal-Plane-Scanning (FPS-OPT) data but it requires to accurately know the system's Point Spread ...

IEEE2021

DeepFocus: a Few-shot Microscope Slide Auto-Focus using a Sample Invariant CNN-based Sharpness Function

Michael Stefan Daniel Liebling, Adrian Shajkofci

Autofocus (AF) methods are extensively used in biomicroscopy, for example to acquire timelapses, where the imaged objects tend to drift out of focus. AF algorithms determine an optimal distance by which to move the sample back into the focal plane. Current ...

2020

Temporal resolution doubling in fluorescence light-sheet microscopy via a hue-encoded shutter and regularization

Michael Stefan Daniel Liebling, Christian Jaques

Studying dynamic biological processes, such as heart development and function in zebrafish embryos, often relies on multi-channel fluorescence labeling to distinguish multiple anatomical features, yet also demands high frame rates to capture rapid cell mot ...

2020

Free annotated data for deep learning in microscopy? A hitchhiker's guide

Michael Stefan Daniel Liebling, Adrian Shajkofci

2020

Aliasing mitigation in optical microscopy of dynamic biological samples by use of temporally modulated color illumination and a standard RGB camera

Michael Stefan Daniel Liebling, Christian Jaques

Significance: Despite recent developments in microscopy, temporal aliasing can arise when imaging dynamic samples. Modern sampling frameworks, such as generalized sampling, mitigate aliasing but require measurement of temporally overlapping and potentially ...

SPIE Society of Photo-optical Instrumentation Engineers2020

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

Temporal Super-Resolution Microscopy Using a Hue-Encoded Shutter

Michael Stefan Daniel Liebling, Sylvain Calinon, Christian Jaques, Emmanuel Pignat

Limited time-resolution in microscopy is an obstacle to many biological studies. Despite recent advances in hardware, digital cameras have limited operation modes that constrain frame-rate, integration time, and color sensing patterns. In this paper, we pr ...

2019

Reconstruction of image sequences from ungated and scanning-aberrated laser scanning microscopy images of the beating heart

Michael Stefan Daniel Liebling, Olivia Mariani

Fluorescence laser-scanning microscopy is a well-established imaging technique in biology, available in many imaging facilities to investigate structures within live animal embryos such as zebrafish. Laser scanning microscopes (LSM) are limited when used t ...

2020

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

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

Direct inversion algorithm for focal plane scanning optical projection tomography

Michael Stefan Daniel Liebling

2017

Simultaneous temporal superresolution and denoising for cardiac fluorescence microscopy

Michael Stefan Daniel Liebling

Due to low light emission of fluorescent samples, live fluorescence microscopy imposes a tradeoff between spatiotemporal resolution and signal-to-noise ratio. This can result in images and videos containing motion blur or Poisson-type shot noise, depending ...

2016

A Point-Spread-Function-Aware Filtered Backprojection Algorithm for Focal-Plane-Scanning Optical Projection Tomography

Michael Stefan Daniel Liebling

Traditional optical projection tomography requires the use of low numerical aperture objectives in order to achieve a large depth of field and approximate parallel projection geometry. However, low NA objectives suffer from poor resolution, resulting in bl ...

2016

Dynamic structure and protein expression of the live embryonic heart captured by 2-photon light sheet microscopy and retrospective registration

Michael Stefan Daniel Liebling

We present an imaging and image reconstruction pipeline that captures the dynamic three-dimensional beating motion of the live embryonic zebrafish heart at subcellular resolution. Live, intact zebrafish embryos were imaged using 2-photon light sheet micros ...

2015

Comparing Algorithms for Reconstructing Digital Off-Axis Fresnel Holograms

Michael Stefan Daniel Liebling, Michaël Unser

Three-dimensional information about an object, such as its depth, may be captured and stored digitally in a single, two-dimensional, real-valued hologram acquired in an off-axis geometry. Digital reconstruction of the hologram permits the quantitative retr ...

SPIE2005

Continuous Wavelet Transform Ridge Extraction for Spectral Interferometry Imaging

Michael Stefan Daniel Liebling, Michaël Unser, Theo Lasser

The combination of wavelength multiplexing and spectral interferometry allows for the encoding of multidimensional information and its transmission over a mono-dimensional channel; for example, measurements of a surface's topography acquired through a mono ...

SPIE2005