Daniel Sage

Address	EPFL STI-IMT-LIB, BM 4.135, Station 17, CH-1015 Lausanne, Switzerland
Tel.	41 21 693 51 89
Fax.	41 21 693 68 10
Email	daniel.sage@epfl.ch
Web page	http://bigwww.epfl.ch/sage/
Office	BM 4.135

Publications

Infoscience publications

Infoscience

Revisiting PSF models: Unifying framework and high‐performance implementation

Y. Liu; V. Stergiopoulou; J. Chuah Wen Jie; E. Bezzam; G. Both et al.

Journal of Microscopy. 2025. DOI : 10.1111/jmi.70045.

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Image Processing and Image Analysis in Microscopy

D. Sage; A. Badoual

Photonic Imaging for Biology: From Conventional Microscopy to Super-Resolution; John Wiley and Sons Inc., 2025. p. 205 - 237.

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

M. Erard; C. Favard; L. D. Lavis; G. Recher; H. Rigneault et al.

Journal of cell science. 2024. DOI : 10.1242/jcs.262344.

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Surpassing light inhomogeneities in structured-illumination microscopy with FlexSIM

E. Soubies; A. Nogueron; F. Pelletier; T. Mangeat; C. Leterrier et al.

Journal of microscopy. 2024. DOI : 10.1111/jmi.13344.

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

C. G. L. de Haro; S. Dallongeville; T. Musset; E. Gomez-de-Mariscal; D. Sage et al.

Nature Methods. 2024. DOI : 10.1038/s41592-023-02129-x.

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A framework for evaluating the performance of SMLM cluster analysis algorithms

D. J. Nieves; J. A. Pike; F. Levet; D. J. Williamson; M. Baragilly et al.

Nature Methods. 2023. DOI : 10.1038/s41592-022-01750-6.

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Correction of multiple-blinking artifacts in photoactivated localization microscopy

L. G. Jensen; T. Y. Hoh; D. J. Williamson; J. Griffie; D. Sage et al.

Nature Methods. 2022. DOI : 10.1038/s41592-022-01463-w.

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

V. Uhlmann; Z. Puspoki; A. Depeursinge; M. Unser; D. Sage et al.

Bioinformatics. 2022. DOI : 10.1093/bioinformatics/btac270.

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

V. Uhlmann; L. Donati; D. Sage

Ieee Signal Processing Magazine. 2022. DOI : 10.1109/MSP.2021.3123589.

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

E. Gomez-de-Mariscal; C. Garcia-Lopez-de-Haro; W. Ouyang; L. Donati; E. Lundberg et al.

Nature Methods. 2021. DOI : 10.1038/s41592-021-01262-9.

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

Q. Juppet; F. De Martino; E. Marcandalli; M. Weigert; O. Burri et al.

Journal of Mammary Gland Biology and Neoplasia. 2021. DOI : 10.1007/s10911-021-09485-4.

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Optimal-Transport-Based Metric for SMLM

Q. A. Denoyelle; T.-A. M. Pham; P. del Aguila Pla; D. Sage; M. Unser

2021. 18th IEEE International Symposium on Biomedical Imaging (ISBI'21), Nice, France, April 13-16, 2021. p. 797 - 801. DOI : 10.1109/ISBI48211.2021.9433874.

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

M. Pourya; S. Aziznejad; M. Unser; D. Sage

2021. 18th IEEE International Symposium on Biomedical Imaging (ISBI), Nice, FRANCE, Apr 13-16, 2021. p. 1892 - 1896. DOI : 10.1109/ISBI48211.2021.9433760.

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

V. Petrenko; N. R. Gandasi; D. Sage; A. Tengholm; S. Barg et al.

Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2020. DOI : 10.1073/pnas.1916539117.

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

R. Zhou; M. El Helou; D. Sage; T. Laroche; A. Seitz et al.

2020. ECCV 2020 Workshop on BioImage Computing, Glasgow, United Kingdom, August 23-28, 2020. p. 499 - 518. DOI : 10.1007/978-3-030-67070-2_30.

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Reconstruction Methods for Cryo-Electron Microscopy: From Model-based to Data-driven

L. Donati / M. Unser; D. Sage (Dir.)

Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7540.

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Pocket guide to solve inverse problems with GlobalBioIm

E. Soubies; F. Soulez; M. T. McCann; Thanh-an Pham; L. Donati et al.

Inverse Problems. 2019. DOI : 10.1088/1361-6420/ab2ae9.

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

D. Sage; Thanh-An Pham; H. Babcock; T. Lukes; T. Pengo et al.

Nature Methods. 2019. DOI : 10.1038/s41592-019-0364-4.

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Deforming Tessellations for the Segmentation of Cell Aggregates

A. Badoual; A. A. Galan; D. Sage; M. Unser

2019. Sixteenth IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI'19), Venice, Italian Republic, April 8-11, 2019. p. 1013 - 1017. DOI : 10.1109/ISBI.2019.8759311.

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

T.-a. Pham; E. Soubies; D. Sage; M. Unser

2019. Sixteenth IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI'19), Venice, Italian Republic, April 8-11, 2019. p. 321 - 324. DOI : 10.1109/ISBI.2019.8759279.

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SUBDIVIDE AND CONQUER Active Contours and Surfaces for Biomedical Image Segmentation

A. L. M.-T. Badoual / M. Unser; D. Sage (Dir.)

Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9326.

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A mobile measurement platform and an image processing procedure for high-resolution aerial thermal imagery of lake surface water temperatures

A. Irani Rahaghi; U. Lemmin; D. Sage; D. A. Barry

International Association for Great Lakes Research & European Large Lakes Symposium (ELLS-IAGLR 2018), Evian, France, 23-28 September 2018.

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Pancreatic α- and β-Cellular Clocks Have Distinct Molecular Properties and Impact on Islet Hormone Secretion and Gene Expression

V. Petrenko; C. Saini; L. Giovannoni; C. Gobet; D. Sage et al.

Genes & Development. 2017. DOI : 10.1101/gad.290379.116.

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DeconvolutionLab2: An Open-Source Software for Deconvolution Microscopy

D. Sage; L. Donati; F. Soulez; D. Fortun; G. Schmit et al.

Methods—Image Processing for Biologists. 2017. DOI : 10.1016/j.ymeth.2016.12.015.

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Parametric Experimental Study and Design of Experiment Modelling of Sapphire Grinding

K. Wasmer; P.-M. Pochon; D. Sage; J. Giovanola

Journal of Cleaner Production. 2017. DOI : 10.1016/j.jclepro.2016.09.031.

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Spline Shape Processing : Representation, Learning, and Modeling

D. A. Schmitter / M. Unser; D. Sage (Dir.)

Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-8174.

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Investigating Focal Adhesion Substructures by Localization Microscopy

H. Deschout; I. Platzman; D. Sage; L. Feletti; J. P. Spatz et al.

Biophysical Journal. 2017. DOI : 10.1016/j.bpj.2017.09.032.

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Transforms and Operators for Directional Bioimage Analysis: A Survey

Z. Püspöki; M. K. Storath; D. Sage; M. Unser

Advances in Anatomy, Embryology and Cell Biology; Springer International Publishing, 2016.

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Variational Phase Imaging Using the Transport-of-Intensity Equation

E. Bostan; E. Froustey; M. Nilchian; D. Sage; M. Unser

IEEE Transactions on Image Processing. 2016. DOI : 10.1109/TIP.2015.2509249.

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A Feasability Study of Color Flow Doppler Vectorization for Automated Blood Flow Monitoring

R. Schorer; A. Badoual; B. Bastide; A. Vandebrouck; M. Licker et al.

Journal of Clinical Monitoring and Computing. 2016. DOI : 10.1007/s10877-016-9953-2.

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Super-Resolution Fight Club

S. Holden; D. Sage

Nature Photonics. 2016. DOI : 10.1038/nphoton.2016.22.

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SpotCaliper: Fast Wavelet-Based Spot Detection with Accurate Size Estimation

Z. Püspöki; D. Sage; J. P. Ward; M. Unser

Bioinformatics. 2016. DOI : 10.1093/bioinformatics/btv728.

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On the Continuous Steering of the Scale of Tight Wavelet Frames

Z. Püspöki; J. Ward; D. Sage; M. Unser

SIAM Journal on Imaging Sciences. 2016. DOI : 10.1137/15M1033885.

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A Simple, Fast and Low-Cost Method for in situ Monitoring of Topographical Changes and Wear Rate of a Complex Tribo-System Under Mixed Lubrication

B. Meylan; P. Dogan; D. Sage; K. Wasmer

Wear—An International Journal on the Science and Technology of Friction, Lubrication and Wear. 2016. DOI : 10.1016/j.wear.2016.06.006.

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Quantitative evaluation of software packages for single-molecule localization microscopy

D. Sage; H. Kirshner; T. Pengo; N. Stuurman; J. Min et al.

Nature Methods. 2015. DOI : 10.1038/Nmeth.3442.

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Analysis of S. pombe SIN protein association to the SPB reveals two genetically separable states of the SIN

P. Wachowicz; A. Chasapi; A. Krapp; E. C. Del Rosario; D. Schmitter et al.

Journal Of Cell Science. 2015. DOI : 10.1242/jcs.160150.

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Fast Detection and Refined Scale Estimation Using Complex Isotropic Wavelets

Z. Püspöki; J. Ward; D. Sage; M. Unser

2015. p. 512 - 515. DOI : 10.1109/ISBI.2015.7163923.

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Phase Retrieval by Using Transport-of-Intensity Equation and Differential Interference Contrast Microscopy

E. Bostan; E. Froustey; B. Rappaz; É. Shaffer; D. Sage et al.

2014. p. 3939 - 3943. DOI : 10.1109/ICIP.2014.7025800.

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Photobleaching Kinetics and Time-Integrated Emission of Fluorescent Probes in Cellular Membranes

D. Wustner; T. Christensen; L. M. Solanko; D. Sage

Molecules. 2014. DOI : 10.3390/molecules190811096.

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Autonomous and self-sustained circadian oscillators displayed in human islet cells

P. Pulimeno; T. Mannic; D. Sage; L. Giovannoni; P. Salmon et al.

Diabetologia. 2013. DOI : 10.1007/s00125-012-2779-7.

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Benchmarking Image-Processing Algorithms for Biomicroscopy: Reference Datasets and Perspectives

D. Sage; H. Kirshner; C. Vonesch; S. Lefkimmiatis; M. Unser

2013.

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Advanced Image Processing for Biology, and the Open Bio Image Alliance (OBIA)

M. Unser; D. Sage; R. Delgado-Gonzalo

2013.

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3-D PSF fitting for fluorescence microscopy: implementation and localization application

H. Kirshner; F. Aguet; D. Sage; M. Unser

Journal Of Microscopy. 2013. DOI : 10.1111/j.1365-2818.2012.03675.x.

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Circadian Clock Characteristics Are Altered in Human Thyroid Malignant Nodules

T. Mannic; P. Meyer; F. Triponez; M. Pusztaszeri; G. Le Martelot et al.

Journal Of Clinical Endocrinology & Metabolism. 2013. DOI : 10.1210/jc.2013-2568.

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A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis

D. Schmitter; P. Wachowicz; D. Sage; A. Chasapi; I. Xenarios et al.

Cell Division. 2013. DOI : 10.1186/1747-1028-8-6.

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Experimental investigation of collagen waviness and orientation in the arterial adventitia using confocal laser scanning microscopy

R. Rezakhaniha; A. Agianniotis; J. T. C. Schrauwen; A. Griffa; D. Sage et al.

Biomechanics and Modeling in Mechanobiology. 2012. DOI : 10.1007/s10237-011-0325-z.

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Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation

D. Wuestner; L. M. Solanko; F. W. Lund; D. Sage; H. J. Schroll et al.

Bmc Bioinformatics. 2012. DOI : 10.1186/1471-2105-13-296.

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A Psf-Based Approach To Biplane Calibration In 3D Super-Resolution Microscopy

H. Kirshner; T. Pengo; N. Olivier; D. Sage; S. Manley et al.

2012. 9th IEEE International Symposium on Biomedical Imaging (ISBI) - From Nano to Macro. p. 1232 - 1235. DOI : 10.1109/ISBI.2012.6235784.

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Predicting stem cell fate changes by differential cell cycle progression patterns

M. Roccio; D. Schmitter; M. Knobloch; Y. Okawa; D. Sage et al.

Development. 2012. DOI : 10.1242/dev.086215.

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Bi-Exponential Edge-Preserving Smoother

P. Thevenaz; D. Sage; M. Unser

Ieee Transactions On Image Processing. 2012. DOI : 10.1109/Tip.2012.2200903.

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Flow measurements in sewer systems based on image analysis: automatic flow velocity algorithm

D. Jeanbourquin; D. Sage; L. S. Nguyen; B. Schaeli; S. Kayal et al.

Water Science and Technology. 2011. DOI : 10.2166/wst.2011.176.

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Fast O(1) Bilateral Filtering Using Trigonometric Range Kernels

K. N. Chaudhury; D. Sage; M. Unser

IEEE Transactions on Image Processing. 2011. DOI : 10.1109/TIP.2011.2159234.

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Potential of Ultraviolet Wide-Field Imaging and Multiphoton Microscopy for Analysis of Dehydroergosterol in Cellular Membranes

D. Wustner; J. R. Brewer; L. Bagatolli; D. Sage

Microscopy Research And Technique. 2011. DOI : 10.1002/jemt.20878.

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Comparison of Deconvolution Software in 3D Microscopy: A User Point of View—Part 1

A. Griffa; N. Garin; D. Sage

G.I.T. Imaging & Microscopy. 2010.

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Comparison of Deconvolution Software: A User Point of View—Part 2

A. Griffa; N. Garin; D. Sage

G.I.T. Imaging & Microscopy. 2010.

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Flow Measurements in Sewer Systems Based on Image Analysis: Automatic Flow Velocity Algorithm

D. Jeanbourquin; D. Sage; L. Nguyen; B. Schaeli; S. Kayal et al.

2010. p. 180 - 189.

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Multicolor Bleach-Rate Imaging Enlightens in vivo Sterol Transport

D. Wüstner; D. Sage

Communicative & Integrative Biology. 2010. DOI : 10.4161/cib.3.4.11972.

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Selective Visualization of Fluorescent Sterols in Caenorhabditis elegans by Bleach-Rate-Based Image Segmentation

D. Wüstner; A. Larsen; N. Færgeman; J. Brewer; D. Sage

Traffic. 2010. DOI : 10.1111/j.1600-0854.2010.01040.x.

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Fast Detection of Cells Using a Continuously Scalable Mexican-Hat-Like Template

K. Chaudhury; Z. Püspöki; A. Muñoz Barrutia; D. Sage; M. Unser

2010. 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Rotterdam, NETHERLANDS, Apr 14-17, 2010. p. 1277 - 1280. DOI : 10.1109/ISBI.2010.5490229.

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Flow measurements in sewer systems based on image analysis: automatic flow velocity algorithm

D. Jeanbourquin; D. Sage; L. Nguyen; B. Schaeli; S. Kayal et al.

2010. 7th International conference on sustainable techniques and strategies in urban water management (NOVATECH), Lyon, France, June 27 - July 1st, 2010.

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Low-Bond Axisymmetric Drop Shape Analysis for Surface Tension and Contact Angle Measurements of Sessile Drops

A. Stalder; T. Melchior; M. Müller; D. Sage; T. Blu et al.

Colloids and Surfaces A: Physicochemical and Engineering Aspects. 2010. DOI : 10.1016/j.colsurfa.2010.04.040.

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A software solution for recording circadian oscillator features in time-lapse live cell microscopy

D. Sage; M. Unser; P. Salmon; C. Dibner

Cell Division. 2010. DOI : 10.1186/1747-1028-5-17.

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Vision-Based System for the Control and Measurement of Wastewater Flow Rate in Sewer Systems

L. Nguyen; D. Sage; S. Kayal; D. Jeanbourquin; M. Scherz et al.

2009. p. OP03 - 4.

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Phosphorylation does not prompt, nor prevent, the formation of alpha-synuclein toxic species in a rat model of Parkinson's disease

S. Azeredo da Silveira; B. Schneider; C. Cifuentes-Diaz; D. Sage; T. Abbas-Terki et al.

Human Molecular Genetics. 2009. DOI : 10.1093/hmg/ddn417.

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Circadian gene expression is resilient to large fluctuations in overall transcription rates

C. Dibner; D. Sage; M. Unser; C. Bauer; T. d'Eysmond et al.

The EMBO journal. 2009. DOI : 10.1038/emboj.2008.262.

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Effect of aging on elastin functionality in human cerebral arteries

E. Fonck; G. G. Feigl; J. Fasel; D. Sage; M. Unser et al.

Stroke; a journal of cerebral circulation. 2009. DOI : 10.1161/STROKEAHA.108.528091.

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Vision-based system for the control and measurement of wastewater flow rate in sewer systems

L. Nguyen; B. Schaeli; D. Sage; S. Kayal; D. Jeanbourquin et al.

Water Science and Technology. 2009. DOI : 10.2166/wst.2009.659.

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Multiresolution Monogenic Signal Analysis Using the Riesz-Laplace Wavelet Transform

M. Unser; D. Sage; D. Van De Ville

Ieee Transactions On Image Processing. 2009. DOI : 10.1109/TIP.2009.2027628.

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Effect of Ageing on Elastin Functionality in Human Cerebral Arteries

E. Fonck; G. Feigl; J. Fasel; D. Sage; M. Unser et al.

2008. ASME 2008 Summer Bioengineering Conference (SBC'08), Marco Island FL, USA, June 25–29, 2008. p. 959 - 960. DOI : 10.1115/SBC2008-192727.

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Controlled Exchange of Chromosomal Arms Reveals Principles Driving Telomere Interactions in Yeast

H. Schober; V. Kalck; M. Vega-Palas; G. Van Houwe; D. Sage et al.

Genome Research. 2008. DOI : 10.1101/gr.6687808.

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The Marr Wavelet Pyramid and Multiscale Directional Image Analysis

D. Van De Ville; D. Sage; K. Balać; M. Unser

2008.

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Coupled tomography and distinct-element-method approach to exploring the granular media microstructure in a jamming hourglass

M. Tsukahara; S. Mitrovic; V. Gajdosik; G. Margaritondo; L. Pournin et al.

Physical Review E. 2008. DOI : 10.1103/PhysRevE.77.061306.

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Selective visualization of fluorescent sterols in Caenorhabditis elegans

D. Wustner; A. L. Larsen; J. R. Brewer; D. Sage; N. J. Faergeman

2008. 49th International Conference on the Bioscience of Lipids, Maastricht, NETHERLANDS, Aug 26-30, 2008. p. S42 - S42. DOI : 10.1016/j.chemphyslip.2008.05.114.

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Lung Tissue Classification Using Wavelet Frames

A. Depeursinge; D. Sage; A. Hidki; A. Platon; P.-A. Poletti et al.

2007. p. 6259 - 6262. DOI : 10.1109/IEMBS.2007.4353786.

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A Snake-Based Approach to Accurate Determination of Both Contact Points and Contact Angles

A. Stalder; G. Kulik; D. Sage; L. Barbieri; P. Hoffmann

Colloids And Surfaces A: Physicochemical And Engineering Aspects. 2006. DOI : 10.1016/j.colsurfa.2006.03.008.

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IP-LAB: A Tool to Teach Image Processing Programming in Java—Challenge in Swiss Federal Institute of Technology Lausanne

平. (A. Hirabayashi); D. Sage; M. Unser

2005. p. 473 - 474.

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Image Processing Education

U. Rajashekar; A. Bovik; D. Sage; M. Unser; L. Karam et al.

Handbook of Image & Video Processing (Second Edition); Amsterdam, The Netherlands: Elsevier Academic Press, 2005. p. 73 - 95.

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PixFRET, an ImageJ Plug-in for FRET Calculation That Can Accommodate Variations in Spectral Bleed-throughs

J. Feige; D. Sage; W. Wahli; B. Desvergne; L. Gelman

Microscopy Research and Technique. 2005. DOI : 10.1002/jemt.20215.

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Analyse des caractéristiques géométriques d'amas granulaires réels et simulés

T. Christe; T. Liebling; L. Pournin; D. Sage

2005

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Automatic Tracking of Individual Fluorescence Particles: Application to the Study of Chromosome Dynamics

D. Sage; F. Neumann; F. Hediger; S. Gasser; M. Unser

IEEE Transactions on Image Processing. 2005. DOI : 10.1109/TIP.2005.852787.

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Extended Depth-of-Field for Color Images in Light Microscopy: Image Fusion and 3D Visualization

B. Forster; D. Van De Ville; J. Berent; N. Quack; D. Sage et al.

Proceedings of the 2004 Annual Meeting of the Swiss Society of Biomedical Engineering (SSBE'04), Zürich, Switzerland, September 2-3, 2004.

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Extended Depth-of-Focus for Multi-Channel Microscopy Images: A Complex Wavelet Approach

B. Forster; D. Van De Ville; J. Berent; D. Sage; M. Unser

2004. p. 660 - 663. DOI : 10.1109/ISBI.2004.1398624.

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Complex Wavelets for Extended Depth-of-Field: A New Method for the Fusion of Multichannel Microscopy Images

B. Forster; D. Van De Ville; J. Berent; D. Sage; M. Unser

Microscopy Research and Technique. 2004. DOI : 10.1002/jemt.20092.

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Automatic Tracking of Particles in Dynamic Fluorescence Microscopy

D. Sage; F. Hediger; S. Gasser; M. Unser

2003. p. 582 - 586. DOI : 10.1109/ISPA.2003.1296963.

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Teaching Image-Processing Programming in Java

D. Sage; M. Unser

IEEE Signal Processing Magazine. 2003. DOI : 10.1109/MSP.2003.1253553.

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Easy Java Programming for Teaching Image Processing

D. Sage; M. Unser

2001. p. 298 - 301. DOI : 10.1109/ICIP.2001.958110.

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