Biomedical Imaging Group

Daniel Sage

Daniel Sage is a specialist of open-source imaging software for various modalities of microscopy, including super-resolution microscopy, deconvolution, image restoration, tracking, segmentation, and image quantification. He is involved in numerous image-processing and image-analysis projects dealing with life cell imaging. He is also engaged in the development of methods for computer-assisted teaching.

Daniel Sage was born in Annecy, France. After his university degree, he did a Ph.D. in image processing at the TIRF laboratory, Institut National Polytechnique de Grenoble (INPG). From 1989 to 1998, he was a Consulting Engineer developing vision systems for quality control, then Head of the Industrial Vision Department of Attexor S.A. During his career, he has developed some vision systems oriented to the quality control in the industrial sector. In 1998, he joined the Biomedical Imaging Group (BIG) at Ecole Polytechnique Fédérale de Lausanne (EPFL) as responsible of software development. He is in charge of both the coordination of software development and of setting down the computing infrastructure of the laboratory.

Address: | EPFL STI-IMT-LIB, Station 17, CH-1015 Lausanne, Switzerland |

Office: | BM 4.135 |

Location: | |

Phone: | +41 21 693 51 89 (EPFL) or +41 21 691 54 25 (Ecublens) |

Email: | daniel.sage@epfl.ch |

Affiliation: |

Color-coded orientation (OrientationJ)

Color-coded orientation (OrientationJ)

Tracking of bioluminescent cells

Building of realistic point-spread function

Fast Laplacian of Gaussian filter

Super-resolution Microscopy

Single-Molecule Localization Microscopy (SMLM/PALM/STORM)

- ISBI 2013 Challenge: Benchmarking of SMLM software on reference datasets
- SMLM 2016 Challenge: Benchmarking of 3D SMLM software
- Reference PDF: Sage et al., Nature Methods, vol. 12, 2015

3D Deconvolution Microscopy

- DeconvolutionLab2: A Java software for deconvolution
- PSF Generator: Generates theoretical point-spread function
- Reference PDF: Sage et al., Elsevier Methods, vol. 115, 2017

Biological Imaging Software Tools

Java ImageJ Plugins

- SpotTracker: Tracking single particle over noisy images sequence
- EDF: Extended depth of field
- Graylevel Watershed: Watershed segmentation on graylevel images
- Spot Enhancing Filter: 3D Laplacian of Gaussian filter
- Spot Distance: Intra-nuclear 3D cross-distances in fluorescent channels
- OrientationJ: Directional image analysis, measure, vector fields
- PixBleach: Pixelwise analysis of photobleaching rate
- PixFRET: FRET calculation for variations in spectral bleed-throughs

Projects

Educational

- Online Demo: Javascript/HTML5 image-processing demonstrations
- IP-LAB: Teaching image-processing programming in Java
- Applet Demo: Java applets for image-processing demonstrations
- Reference PDF: Sage et al., IEEE Signal Processing magazine, vol. 20, 2003

Life Science

- SNSF Synegia: Coordination of mitosis and cytokinesis
- Circadian: Circadian gene expression recording
- Directional Image Analysis: MonogenicJ and OrientationJ

Material Science

- Drop Shape Analysis: Contact angle measurement
- Tribology: Collaboration with EMPA

Environmental Science

- HydroPix Monitoring: Visual monitoring of the sewer systems (CTI)
- Wind Device Measurement CTI project

Useful Algorithms as ImageJ Plugins

- MIJ: Bi-directional communication and data exchange from Matlab to ImageJ
- SNR: Evaluation of the similarity of two images
- LoG 3D: Fast Laplacian of Gaussian in 3D
- Local Normalization: Compensation of non-uniformities
- Smoothing Filters: Comparison of smoothing routines

- Microscopy Image Restoration: DeconvolutionLab2

NEUBIAS Training School for Early Career Investigators, 2017, Oeiras, Portugal - Computational Methods for High Resolution 3D Fluorescence Microscopy

The BioImage Analysis Community Conference (NEUBIAS2020) 2017, Lisbon, Portugal - Image Processing and Image Analysis for Light Microscopy

Invited Seminar at the Center of Genomic Regulation, 2016, Barcelona, Spain - Open Software Tools for Microscopy Image Processing

ELMI 2016, Debrecen, Hungary - ImageJ for Biologists

Course b.Image 2014, Porto, Portugal - Basic Image-Processing - Life Science Applications

INCF Short Course 2013, Antwerp, Belgium - Analysis in Live Cell Imaging - ImageJ/Fiji Solutions

Bioimage 2012, Porto, Portugal - Bioimage Analysis Software: Is there a Future Beyond ImageJ?

Eurobioimaging meeting 2012, Barcelona, Spain - Signal-Processing Algorithms for Bioimaging

SPCOM 2010, Bangalore, India

Journal Articles

D. Sage, F. Soulez, "Computational Methods for High Resolution 3D Fluorescence Microscopy," The BioImage Analysis Community Conference "Workflows and Open Tools" (NEUBIAS2020'17), Lisbon, Portuguese Republic, February 12-17, 2017, in press.

V. Petrenko, C. Saini, L. Giovannoni, C. Gobet, D. Sage, M. Unser, M.H. Masson, G. Gu, D. Bosco, F. Gachon, J. Philippe, C. Dibner, "Pancreatic α- and β-Cellular Clocks Have Distinct Molecular Properties and Impact on Islet Hormone Secretion and Gene Expression," Genes & Development, vol. 31, no. 4, pp. 383-398, February 15, 2017.

D. Sage, L. Donati, F. Soulez, D. Fortun, G. Schmit, A. Seitz, R. Guiet, C. Vonesch, M. Unser, "DeconvolutionLab2: An Open-Source Software for Deconvolution Microscopy," Methods—Image Processing for Biologists, vol. 115, pp. 28-41, February 15, 2017.

K. Wasmer, P.-M. Pochon, D. Sage, J.H. Giovanola, "Parametric Experimental Study and Design of Experiment Modelling of Sapphire Grinding," Journal of Cleaner Production, vol. 141, pp. 323-335, January 10, 2017.

R. Schorer, A. Badoual, B. Bastide, A. Vandebrouck, M. Licker, D. Sage, "A Feasability Study of Color Flow Doppler Vectorization for Automated Blood Flow Monitoring," Journal of Clinical Monitoring and Computing, article not assigned to an issue, pp. 1-9, November 12, 2016.

B. Meylan, P. Dogan, D. Sage, K. Wasmer, "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," Wear—An International Journal on the Science and Technology of Friction, Lubrication and Wear, vol. 364-365, pp. 22-30, October 15, 2016.

Z. Püspöki, M. Storath, D. Sage, M. Unser, "Transforms and Operators for Directional Bioimage Analysis: A Survey," Advances in Anatomy, Embryology and Cell Biology, vol. 219, Springer International Publishing, ch. 3, pp. 69-93, May 21, 2016.

Z. Püspöki, D. Sage, J.P. Ward, M. Unser, "SpotCaliper: Fast Wavelet-Based Spot Detection with Accurate Size Estimation," Bioinformatics, vol. 32, no. 8, pp. 1278-1280, April 15, 2016.

S. Holden, D. Sage, "Super-Resolution Fight Club," Nature Photonics, vol. 10, no. 3, pp. 152-153, March 2016.

E. Bostan, E. Froustey, M. Nilchian, D. Sage, M. Unser, "Variational Phase Imaging Using the Transport-of-Intensity Equation," IEEE Transactions on Image Processing, vol. 25, no. 2, pp. 807-817, February 2016.

Z. Püspöki, J.P. Ward, D. Sage, M. Unser, "On the Continuous Steering of the Scale of Tight Wavelet Frames," SIAM Journal on Imaging Sciences, vol. 9, no. 3, pp. 1042-1062, 2016.

D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, M. Unser, "Quantitative Evaluation of Software Packages for Single-Molecule Localization Microscopy," Nature Methods, vol. 12, no. 8, pp. 717-724, August 2015.

P. Wachowicz, A. Chasapi, A. Krapp, E.C. del Rosario, D. Schmitter, D. Sage, M. Unser, I. Xenarios, J. Rougemont, V. Simanis, "Analysis of *S. pombe* SIN Protein Association to the SPB Reveals Two Genetically Separable States of the SIN," Journal of Cell Science, vol. 128, no. 4, pp. 741-754, February 15, 2015.

D. Wüstner, T. Christensen, L.M. Solanko, D. Sage, "Photobleaching Kinetics and Time-Integrated Emission of Fluorescent Probes in Cellular Membranes," Molecules, vol. 19, no. 8, pp. 11096-11130, August 2014.

T. Mannic, P. Meyer, F. Triponez, M. Pusztaszeri, G. Le Martelot, O. Mariani, D. Schmitter, D. Sage, J. Philippe, C. Dibner, "Circadian Clock Characteristics Are Altered in Human Thyroid Malignant Nodules," The Journal of Clinical Endocrinology & Metabolism, vol. 98, no. 11, pp. 4446-4456, November 2013.

D. Schmitter, P. Wachowicz, D. Sage, A. Chasapi, I. Xenarios, V. Simanis, M. Unser, "A 2D/3D Image Analysis System to Track Fluorescently Labeled Structures in Rod-Shaped Cells: Application to Measure Spindle Pole Asymmetry During Mitosis," Cell Division, vol. 8, no. 6, pp. 1-13, April 27, 2013.

P. Pulimeno, T. Mannic, D. Sage, L. Giovannoni, P. Salmon, S. Lemeille, M. Giry-Laterrière, M. Unser, D. Bosco, C. Bauer, J. Morf, P. Halban, J. Philippe, C. Dibner, "Autonomous and Self-Sustained Circadian Oscillators Displayed in Human Islet Cells," Diabetologia, vol. 56, no. 3, pp. 497-507, March 2013.

M. Roccio, D. Schmitter, M. Knobloch, Y. Okawa, D. Sage, M.P. Lutolf, "Predicting Stem Cell Fate Changes by Differential Cell Cycle Progression Patterns," Development, vol. 140, no. 2, pp. 459-470, January 15, 2013.

H. Kirshner, F. Aguet, D. Sage, M. Unser, "3-D PSF Fitting for Fluorescence Microscopy: Implementation and Localization Application," Journal of Microscopy, vol. 249, no. 1, pp. 13-25, January 2013.

D. Wüstner, L.M. Solanko, F.W. Lund, D. Sage, H.J. Schroll, M.A. Lomholt, "Quantitative Fluorescence Loss in Photobleaching for Analysis of Protein Transport and Aggregation," BMC Bioinformatics, vol. 13, no. 296, 21 p., November 13, 2012.

P. Thévenaz, D. Sage, M. Unser, "Bi-Exponential Edge-Preserving Smoother," IEEE Transactions on Image Processing, vol. 21, no. 9, pp. 3924-3936, September 2012.

D. Sage, "Analyse d'image scientifique, le monde ImageJ," flash informatique, no. 3, pp. 3-7, March 27, 2012.

R. Rezakhaniha, A. Agianniotis, J.T.C. Schrauwen, A. Griffa, D. Sage, C.V.C. Bouten, F.N. van de Vosse, M. Unser, N. Stergiopulos, "Experimental Investigation of Collagen Waviness and Orientation in the Arterial Adventitia Using Confocal Laser Scanning Microscopy," Biomechanics and Modeling in Mechanobiology, vol. 11, no. 3-4, pp. 461-473, 2012.

K.N. Chaudhury, D. Sage, M. Unser, "Fast *O*(1) Bilateral Filtering Using Trigonometric Range Kernels," IEEE Transactions on Image Processing, vol. 20, no. 12, pp. 3376-3382, December 2011.

D. Wüstner, J.R. Brewer, L. Bagatolli, D. Sage, "Potential of Ultraviolet Wide-Field Imaging and Multiphoton Microscopy for Analysis of Dehydroergosterol in Cellular Membranes," Microscopy Research and Technique, vol. 74, no. 1, pp. 92-108, January 2011.

D. Jeanbourquin, D. Sage, L. Nguyen, B. Schaeli, S. Kayal, D.A. Barry, L. Rossi, "Flow Measurements in Sewers Based on Image Analysis: Automatic Flow Velocity Algorithm," Water Science & Technology, vol. 64, no. 5, pp. 1108-1114, 2011.

A. Griffa, N. Garin, D. Sage, "Comparison of Deconvolution Software: A User Point of View—Part 2," G.I.T. Imaging & Microscopy, vol. 12, no. 3, pp. 41-43, August 2010.

A.F. Stalder, T. Melchior, M. Müller, D. Sage, T. Blu, M. Unser, "Low-Bond Axisymmetric Drop Shape Analysis for Surface Tension and Contact Angle Measurements of Sessile Drops," Colloids and Surfaces A: Physicochemical and Engineering Aspects, vol. 364, no. 1-3, pp. 72-81, July 20, 2010.

D. Sage, M. Unser, P. Salmon, C. Dibner, "A Software Solution for Recording Circadian Oscillator Features in Time-Lapse Live Cell Microscopy," Cell Division, vol. 5, no. 17, pp. 1-9, July 6, 2010.

D. Wüstner, D. Sage, "Multicolor Bleach-Rate Imaging Enlightens *in vivo* Sterol Transport," Communicative & Integrative Biology, vol. 3, no. 4, pp. 370-373, July/August 2010.

D. Wüstner, A.L. Larsen, N.J. Færgeman, J.R. Brewer, D. Sage, "Selective Visualization of Fluorescent Sterols in *Caenorhabditis elegans* by Bleach-Rate-Based Image Segmentation," Traffic, vol. 11, no. 4, pp. 440-454, April 2010.

A. Griffa, N. Garin, D. Sage, "Comparison of Deconvolution Software in 3D Microscopy: A User Point of View—Part 1," G.I.T. Imaging & Microscopy, vol. 12, no. 1, pp. 43-45, March 2010.

M. Unser, D. Sage, D. Van De Ville, "Multiresolution Monogenic Signal Analysis Using the Riesz-Laplace Wavelet Transform," IEEE Transactions on Image Processing, vol. 18, no. 11, pp. 2402-2418, November 2009.

E. Fonck, G.G. Feigl, J. Fasel, D. Sage, M. Unser, D.A. Rüfenacht, N. Stergiopulos, "Effect of Aging on Elastin Functionality in Human Cerebral Arteries," Stroke, vol. 40, no. 7, pp. 2552-2556, July 2009.

S.A. da Silveira, B.L. Schneider, C. Cifuentes-Diaz, D. Sage, T. Abbas-Terki, T. Iwatsubo, M. Unser, P. Aebischer, "Phosphorylation Does Not Prompt, Nor Prevent, the Formation of α-Synuclein Toxic Species in a Rat Model of Parkinson's Disease," Human Molecular Genetics, vol. 18, no. 5, pp. 872-887, March 1, 2009.

C. Dibner, D. Sage, M. Unser, C. Bauer, T. d'Eysmond, F. Naef, Ü. Schibler, "Circadian Gene Expression Is Resilient to Large Fluctuations in Overall Transcription Rates," The European Molecular Biology Organization Journal, vol. 28, no. 2, pp. 123-134, January 21, 2009.

L.S. Nguyen, B. Schaeli, D. Sage, S. Kayal, D. Jeanbourquin, D.A. Barry, L. Rossi, "Vision-Based System for the Control and Measurement of Wastewater Flow Rate in Sewer Systems," Water Science & Technology, vol. 60, no. 9, pp. 2281-2289, 2009.

M. Tsukahara, S. Mitrović, V. Gajdosik, G. Margaritondo, L. Pournin, M. Ramaioli, D. Sage, Y. Hwu, M. Unser, T.M. Liebling, "Coupled Tomography and Distinct-Element-Method Approach to Exploring the Granular Media Microstructure in a Jamming Hourglass," Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), vol. 77, no. 6, paper no. 061306, 11 p., June 2008.

H. Schober, V. Kalck, M.A. Vega-Palas, G. Van Houwe, D. Sage, M. Unser, M.R. Gartenberg, S.M. Gasser, "Controlled Exchange of Chromosomal Arms Reveals Principles Driving Telomere Interactions in Yeast," Genome Research, vol. 18, no. 2, pp. 261-271, February 2008.

A.F. Stalder, G. Kulik, D. Sage, L. Barbieri, P. Hoffmann, "A Snake-Based Approach to Accurate Determination of Both Contact Points and Contact Angles," Colloids And Surfaces A: Physicochemical And Engineering Aspects, vol. 286, no. 1-3, pp. 92-103, September 2006.

J.N. Feige, D. Sage, W. Wahli, B. Desvergne, L. Gelman, "PixFRET, an ImageJ Plug-in for FRET Calculation That Can Accommodate Variations in Spectral Bleed-throughs," Microscopy Research and Technique, vol. 68, no. 1, pp. 51-58, September 2005.

D. Sage, F.R. Neumann, F. Hediger, S.M. Gasser, M. Unser, "Automatic Tracking of Individual Fluorescence Particles: Application to the Study of Chromosome Dynamics," IEEE Transactions on Image Processing, vol. 14, no. 9, pp. 1372-1383, September 2005.

B. Forster, D. Van De Ville, J. Berent, D. Sage, M. Unser, "Complex Wavelets for Extended Depth-of-Field: A New Method for the Fusion of Multichannel Microscopy Images," Microscopy Research and Technique, vol. 65, no. 1-2, pp. 33-42, September 2004.

D. Sage, M. Unser, "Teaching Image-Processing Programming in Java," IEEE Signal Processing Magazine, vol. 20, no. 6, pp. 43-52, November 2003.

Conference Papers

Z. Püspöki, J.P. Ward, D. Sage, M. Unser, "Fast Detection and Refined Scale Estimation Using Complex Isotropic Wavelets," IEEE ISBI 2015, Brooklyn NY, USA, April 16-19, 2015.

E. Bostan, E. Froustey, B. Rappaz, É. Shaffer, D. Sage, M. Unser, "Phase Retrieval by Using Transport-of-Intensity Equation and Differential Interference Contrast Microscopy," IEEE ICIP 2014, Paris, France, October 27-30, 2014.

D. Sage, H. Kirshner, C. Vonesch, S. Lefkimmiatis, M. Unser, "Benchmarking Image-Processing Algorithms for Biomicroscopy: Reference Datasets and Perspectives," EUSIPCO 2013, Marrakech, Morocco, September 9-13, 2013.

M. Unser, D. Sage, R. Delgado-Gonzalo, "Advanced Image Processing for Biology, and the Open Bio Image Alliance (OBIA)," EUSIPCO 2013, Marrakech, Morocco, September 9-13, 2013.

H. Kirshner, T. Pengo, N. Olivier, D. Sage, S. Manley, M. Unser, "A PSF-Based Approach to Biplane Calibration in 3D Super-Resolution Microscopy," IEEE ISBI 2012, Barcelona, Spain, May 2-5, 2012.

D. Jeanbourquin, D. Sage, L. Nguyen, B. Schaeli, S. Kayal, D.A. Barry, L. Rossi, "Flow Measurements in Sewer Systems Based on Image Analysis: Automatic Flow Velocity Algorithm," Proceedings of the Seventh International Conference on Sustainable Techniques and Strategies in Urban Water Management (NOVATECH'10), Lyon, France, June 27-July 1.

K.N. Chaudhury, Z. Püspöki, A. Muñoz Barrutia, D. Sage, M. Unser, "Fast Detection of Cells Using a Continuously Scalable Mexican-Hat-Like Template," IEEE ISBI 2010, Rotterdam, The Netherlands, April 14-17, 2010.

L. Nguyen, D. Sage, S. Kayal, D. Jeanbourquin, M. Scherz, D.A. Barry, M. Unser, L. Rossi, "Vision-Based System for the Control and Measurement of Wastewater Flow Rate in Sewer Systems," Proceedings of the Tenth IWA Conference on Instrumentation, Control and Automation (ICA'09), Cairns QLD, Australia, June 14-17, 2009.

D. Van De Ville, D. Sage, K. Balać, M. Unser, "The Marr Wavelet Pyramid and Multiscale Directional Image Analysis," EUSIPCO 2008, Lausanne, Switzerland, August 25-29, 2008.

E. Fonck, G.G. Feigl, J. Fasel, D. Sage, M. Unser, D.A. Rüfenacht, N. Stergiopulos, "Effect of Ageing on Elastin Functionality in Human Cerebral Arteries," Proceedings of the ASME 2008 Summer Bioengineering Conference (SBC'08), Marco Island FL, USA, June 25-29, 2008.

A. Depeursinge, D. Sage, A. Hidki, A. Platon, P.-A. Poletti, M. Unser, H. Müller, "Lung Tissue Classification Using Wavelet Frames," IEEE EMBC 2007, Lyon, France, August 23-26, 2007.

平林 晃 (A. Hirabayashi), D. Sage, M. Unser, "IP-LAB: A Tool to Teach Image Processing Programming in Java—Challenge in Swiss Federal Institute of Technology Lausanne," Proceedings of the Fifty-Third Annual Japanese Society for Engineering Education Conference (JSEE'05), Hiroshima, Japan, September 9-11, 2005.

B. Forster, D. Van De Ville, J. Berent, D. Sage, M. Unser, "Extended Depth-of-Focus for Multi-Channel Microscopy Images: A Complex Wavelet Approach," IEEE ISBI 2004, Arlington VA, USA, April 15-18, 2004.

D. Sage, F. Hediger, S.M. Gasser, M. Unser, "Automatic Tracking of Particles in Dynamic Fluorescence Microscopy," ISPA 2003, Rome, Italy, September 18-20, 2003.

D. Sage, M. Unser, "Easy Java Programming for Teaching Image Processing," IEEE ICIP 2001,Thessaloniki, Greece, October 7-10, 2001.

D. Sage, P.Y. Coulon, "A Contour Feature Tracking System," PInternational Conference On Robot Vision And Sensory Controls (RoViSeC-7), Zürich ZH, Switzerland, February 2-4, 1988.

Conference Abstracts

S. Colabrese, M. Castello, G. Vicidomini, A. Del Bue, D. Sage, "A Study on the Application of Machine Learning Techniques on 2D and 3D SMLM—SMLM Software Challenge," SMLMS 2016, Lausanne, Switzerland, August 28-30, 2016.

D. Sage, "Challenge for Benchmarking Single-Molecule Localization Microscopy Software Packages," SMLMS 2016, Lausanne, Switzerland, August 28-30, 2016.

D. Sage, "Open Software Tools for Microscopy Image Processing," Invited talk, ELMI 2016, Debrecen, Hungary, May 24-27, 2016, p. 47.

N. Chu, R. Nussbaumer, L. Donati, D. Fortun, D. Sage, M. Unser, "A Robust Reconstruction and Pattern Calibration Framework for Structured Illumination Microscopy," 2016 Quantitative BioImaging Conference, Delft, The Netherlands, January 13-15, 2016.

D. Sage, "Bioimage Informatics Algorithms: Detection, Localization, and Tracking Fluorescent Particles," Workshop "Collective Motion of Active Swimmers" (MOTIMO'13), Valbonne, France, September 25-26, 2013.

D. Sage, "Bioimage Informatics: Image-Processing Algorithms and Life-Science Applications," International Neuroinformatics Coordinating Facility Training in Neuroinformatics 2013 (INCF-TN'13), Antwerp, Belgium, September 2-6, 2013.

T. Mannic, P. Meyer, F. Triponez, M. Pusztaszeri, G. Le Martelot, O. Mariani, D. Sage, J. Philippe, C. Dibner, "Circadian Clock Characteristics Are Altered in Human Thyroid Malignant Nodules," Congress of the European Biological Rhythms Society (EBRS'13), Münich, Germany, August 18-22, 2013, pp. 80.

O. Mariani, V. Uhlmann, D. Sage, M. Unser, "BisQuit: Open-Source Interactive Tool for Image Sequence Analysis," Second Swiss Image-Based Screening Conference (SIBSC'13), Lausanne VD, Switzerland, June 10-11, 2013.

D. Sage, D. Prodanov, J.-Y. Tinevez, J. Schindelin, "Daniel Sage: MIJ: Making Interoperability Between ImageJ and Matlab Possible," ImageJ User & Developer Conference (IUDC'12), Mondorf-les-Bains, Luxembourg, October 24-26, 2012.

D. Sage, M. Unser, "From Image-Processing Algorithms to ImageJ Plugins: A Student-Friendly Framework," Workshop within the ImageJ User & Developer Conference (IUDC'12), Mondorf-les-Bains, Luxembourg, October 24-26, 2012.

C. Dibner, T. Mannic, D. Sage, S. Lemeille, D. Bosco, P. Salmon, C. Bauer, M. Unser, P. Halban, J. Philippe, "Robust Circadian Clocks Are Ticking in Beta and non-Beta Cells of Human Pancreatic Islets," Diabetologia, vol. 55, suppl. 1, pp. S115, October 2012.

C. Dibner, T. Mannic, D. Sage, S. Lemeille, D. Bosco, P. Salmon, C. Bauer, M. Unser, P. Halban, J. Philippe, "Robust Circadian Clocks Are Ticking in Beta and non-Beta Cells of Human Pancreatic Islets," Annual Meeting of the European Association for the Study of Diabetes (EASD'12), Berlin, Germany, October 1-5, 2012, paper no. 259, pp. 110.

D. Sage, "Analysis in Live Cell Imaging—ImageJ/Fiji Solutions," International Symposium in Applied Bioimaging: Bridging Development and Application (ISAB'12), Porto, Portugal, September 20-21, 2012, pp. 28.

D. Wüstner, L.M. Solanko, F.W. Lund, D. Sage, H.J. Schroll, M.A. Lomholt, "Quantitative Fluorescence Loss in Photobleaching for Analysis of Protein Transport and Aggregation," Proceedings of BioImage Informatics 2012 (BI'12), Dresden, Germany, September 16-19, 2012, pp. 61-62.

D. Sage, H. Kirshner, T. Pengo, S. Manley, M. Unser, "On the Importance of Simulated Datasets in Localization Microscopy," SSMLMS 2012, Lausanne, Switzerland, August 29-31, 2012.

H. Kirshner, F. Aguet, D. Sage, M. Unser, "Least-Square PSF Fitting for Localization Microscopy," SSMLMS 2012, Lausanne, Switzerland, August 29-31, 2012.

T. Mannic, D. Sage, P. Salmon, J. Philippe, M. Unser, P. Halban, D. Bosco, C. Bauer, C. Dibner, "Étude du rôle de l'horloge circadienne dans la fonction de l'îlot pancréatique humain," Actes de la Vingtième réunion des groupes de recherche en endocrinologie, diabétologie et maladies métaboliques des universités de la région Rhône-Alpes (G2L2'12), Lyon, France, March 30, 2012, pp. 39.

P. Wachowicz, D. Schmitter, D. Sage, M. Unser, L. Cerutti, I. Xenarios, V. Simanis, "Determination of Rules Governing Spindle Pole Asymmetry in SIN Signalling," EMBO Conference Series on Centrosomes & Spindle Pole Bodies (CSPD'11), Barcelona, Spain, October 2-6, 2011.

H. Kirshner, D. Sage, M. Unser, "3D PSF Models for Fluorescence Microscopy in ImageJ," Proceedings of the Twelfth International Conference on Methods and Applications of Fluorescence Spectroscopy, (MAF'11), Strasbourg, France, September 11-14, 2011, pp. 154.

H. Kirshner, T. Pengo, N. Olivier, D. Sage, S. Manley, M. Unser, "Bi-Plane Calibration in Super-Resolution Microscopy," Proceedings of the Twelfth International Conference on Methods and Applications of Fluorescence Spectroscopy, (MAF'11), Strasbourg, France, September 11-14, 2011, pp. 153.

I. Guber, Y. Wimmersberger, D. Sage, F. Majo, "A New Imaging Software to Evaluate the Centration of Capsulorhexis and Intraocular Lens (IOL) After Cataract Surgery," Visionary Genomics (ARVO'11), Fort Lauderdale FL, USA, May 1-5, 2011.

D. Sage, "PALM Localization and Tracking: ImageJ Software Development," First Swiss Photo Activated Localization Microscopy User Meeting (SPALM'10), Zürich, Switzerland, December 17, 2010.

D. Sage, "Daniel Sage: Signal-Processing Algorithms for Bioimaging," ImageJ User & Developer Conference 2010, Mondorf-les-Bains, Luxembourg, October 27-29, 2010.

D. Sage, "Signal-Processing Algorithms for Bioimaging," Tutorial, International Conference on Signal Processing and Communications (SPCOM'10), Bangalore, India, July 18-21, 2010.

C. Dibner, D. Sage, M. Unser, T. d'Eysmond, F. Naef, Ü. Schibler, "On the Robustness of the Mammalian Circadian Oscillator: Dissection of Molecular Mechanisms," The 2009 Gordon Conference on Chronobiology: Molecular Mechanisms of Circadian Clocks (GRC'09), Newport RI, USA, July 19-24, 2009.

L. Nguyen, D. Sage, S. Kayal, D. Jeanbourquin, L. Rossi, "A Vision-Based Tool for the Control of Hydraulic Structures in Sewer System," European Geosciences Union General Assembly 2009, Wien, Austria, April 19-24, 2009.

D. Wüstner, A.L. Larsen, J.R. Brewer, D. Sage, N.J. Færgeman, "Selective Visualization of Fluorescent Sterols in *Caenorhabditis elegans*," Proceedings of the Forty-Ninth International Conference on the Bioscience of Lipids (ICBL'08), Maastricht, The Netherlands, August 26-30, 2008, Chemistry and Physics of Lipids, vol. 154, supp. 1, pp. S42, August 2008.

D. Sage, "Tracking Particles in Live Cell Imaging: ImageJ Solutions," Proceedings of the Sixth FENS Forum of European Neuroscience (FENS-EN'08), Geneva GE, Switzerland, July 12-16, 2008, FENS Abstracts, vol. 4, pp. 003.4.

A. Griffa, T. Laroche, J. Artacho, J.-C.F. Sarria, D. Sage, N. Garin, "Development of Image-Analysis Tools in the BioImaging and Optics Platform (BIOp)," ELMI 2008, Davos, Switzerland, May 27-30, 2008, p. 82.

C. Dibner, D. Sage, Ü. Schibler, M. Unser, "Robust Image Processing Techniques for Tracking and Cell Shape Outlining: Application to Mammalian Circadian Behaviour of Cells," Basel Computational Biology Conference, From Euler to Computational Biology: Integrating Mathematics into Biological Research (USGEB/[BC]^{2}'07), Basel BS, Switzerland, March 13-14, 2007.

I. Mallabiabarrena, C. Prud′homme, A. Radaelli, V. Rigamonti, D. Sage, "From Medical Images to Numerical Blood Flow Simulations in Human Vessels," SSBE 2005, Lausanne, Switzerland, September 1-2, 2005, pp. F21.

A. Beuchat, C.Ó. Sánchez Sorzano, D. Sage, A. Senn, F. Urner, M. Unser, "Multivariate Statistical Analysis and Classification of Zygotes," SSBE 2005, Lausanne, Switzerland, September 1-2, 2005, pp. F04.

B. Forster, D. Van De Ville, J. Berent, N. Quack, D. Sage, M. Unser, "Wavelets for Extended Depth-of-Field in Light Microscopy: Image Fusion and 3D Visualization," Sixth European Conference on Mathematical and Theoretical Biology (ECMTB'05), Dresden, Germany, July 18-22, 2005.

D. Sage, M. Unser, "Automated Tracking of Single Fluorescence Particle," SSBE 2004, Zürich ZH, Switzerland, September 2-3, 2004, poster 55.

B. Forster, D. Van De Ville, J. Berent, N. Quack, D. Sage, M. Unser, "Extended Depth-of-Field for Color Images in Light Microscopy: Image Fusion and 3D Visualization," SSBE 2004, Zürich, Switzerland, September 2-3, 2004, poster 38.

J. Berent, B. Forster, D. Van De Ville, D. Sage, M. Unser, "Extended Depth-of-Focus for Color Images in Bright-Field Microscopy," Autumn Meeting of the Swiss Society of Pharmacology and Toxicology: Imaging Technologies and Their Applications in Pharmacology and Toxicology (ITAPT'03), Basel BS, Switzerland, October 27-28, 2003.

D. Sage, M. Unser, "Automatic Tracking of Particles in Dynamic Fluorescence Microscopy," Autumn Meeting of the Swiss Society of Pharmacology and Toxicology: Imaging Technologies and Their Applications in Pharmacology and Toxicology (ITAPT'03), Basel BS, Switzerland, October 27-28, 2003.

M. Unser, D. Sage, M. Jacob, E. Meijering, P. Thévenaz, "Image Processing and Analysis of Biological Images," Live Cell Imaging Workshop, Lausanne VD, Switzerland, October 9-10, 2002.

Book Chapters

U. Rajashekar, A.C. Bovik, D. Sage, M. Unser, L.J. Karam, R.L. Lagendijk, "Image Processing Education," Handbook of Image & Video Processing (Second Edition), A. Bovik, Ed., Elsevier Academic Press, Amsterdam, The Netherlands, pp. 73-95, 2005.

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