Daniel Sage
EPFL STI IMT LIB
BM 4135 (Bâtiment BM)
Station 17
1015 Lausanne
+41 21 693 51 89
+41 21 693 91 32
Office:
BM 4135
EPFL › STI › IEM › LIB
Website: https://bigwww.epfl.ch/
+41 21 693 91 32
EPFL › SV › SV-SSV › SSV-ENS
Website: https://sv.epfl.ch/education
+41 21 693 91 32
EPFL › STI › STI-SMT › SMT-ENS
EPFL IMAGING
ELE 130 (Bâtiment ELE)
Station 11
1015 Lausanne
+41 21 693 91 32
Office:
BM 4135
EPFL › VPA › VPA-AVP-CP › IMAGING › IMAGING-GE
Expertise
Publications
Publications
Coordinates
Biomedical Imaging Group
AddressEPFL STI-IMT-LIB, BM 4.135, Station 17, CH-1015 Lausanne, Switzerland Tel.+41 21 693 51 89 Fax.+41 21 693 68 10 Emaildaniel.sage@epfl.ch Web pagehttp://bigwww.epfl.ch/sage/ OfficeBM 4.135Infoscience
Roadmap on Deep Learning for Microscopy
JOURNAL OF PHYSICS-PHOTONICS. 2026. DOI : 10.1088/2515-7647/ae0fd1.Revisiting PSF models: Unifying framework and high‐performance implementation
Journal of Microscopy. 2025. DOI : 10.1111/jmi.70045.Image Processing and Image Analysis in Microscopy
Photonic Imaging for Biology: From Conventional Microscopy to Super-Resolution; John Wiley and Sons Inc., 2025. p. 205 - 237.Surpassing light inhomogeneities in structured-illumination microscopy with FlexSIM
Journal of microscopy. 2024. DOI : 10.1111/jmi.13344.Back to the future–20 years of progress and developments in photonic microscopy and biological imaging
Journal of cell science. 2024. DOI : 10.1242/jcs.262344.JDLL: a library to run deep learning models on Java bioimage informatics platforms
Nature Methods. 2024. DOI : 10.1038/s41592-023-02129-x.A framework for evaluating the performance of SMLM cluster analysis algorithms
Nature Methods. 2023. DOI : 10.1038/s41592-022-01750-6.Correction of multiple-blinking artifacts in photoactivated localization microscopy
Nature Methods. 2022. DOI : 10.1038/s41592-022-01463-w.Steer'n'Detect: fast 2D template detection with accurate orientation estimation
Bioinformatics. 2022. DOI : 10.1093/bioinformatics/btac270.A Practical Guide to Supervised Deep Learning for Bioimage Analysis: Challenges and good practices
Ieee Signal Processing Magazine. 2022. DOI : 10.1109/MSP.2021.3123589.DeepImageJ: A user-friendly environment to run deep learning models in ImageJ
Nature Methods. 2021. DOI : 10.1038/s41592-021-01262-9.Deep Learning Enables Individual Xenograft Cell Classification in Histological Images by Analysis of Contextual Features
Journal of Mammary Gland Biology and Neoplasia. 2021. DOI : 10.1007/s10911-021-09485-4.Optimal-Transport-Based Metric for SMLM
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.Graphic: Graph-Based Hierarchical Clustering For Single-Molecule Localization Microscopy
2021. 18th IEEE International Symposium on Biomedical Imaging (ISBI), Nice, FRANCE, Apr 13-16, 2021. p. 1892 - 1896. DOI : 10.1109/ISBI48211.2021.9433760.In pancreatic islets from type 2 diabetes patients, the dampened circadian oscillators lead to reduced insulin and glucagon exocytosis
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2020. DOI : 10.1073/pnas.1916539117.W2S: Microscopy Data with Joint Denoising and Super-Resolution for Widefield to SIM Mapping
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.Reconstruction Methods for Cryo-Electron Microscopy: From Model-based to Data-driven
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7540.Pocket guide to solve inverse problems with GlobalBioIm
Inverse Problems. 2019. DOI : 10.1088/1361-6420/ab2ae9.Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software
Nature Methods. 2019. DOI : 10.1038/s41592-019-0364-4.Deforming Tessellations for the Segmentation of Cell Aggregates
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.SUBDIVIDE AND CONQUER Active Contours and Surfaces for Biomedical Image Segmentation
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9326.Closed-Form Expression of the Fourier Ring-Correlation for Single-Molecule Localization Microscopy
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.A mobile measurement platform and an image processing procedure for high-resolution aerial thermal imagery of lake surface water temperatures
International Association for Great Lakes Research & European Large Lakes Symposium (ELLS-IAGLR 2018), Evian, France, 23-28 September 2018.Parametric Experimental Study and Design of Experiment Modelling of Sapphire Grinding
Journal of Cleaner Production. 2017. DOI : 10.1016/j.jclepro.2016.09.031.Investigating Focal Adhesion Substructures by Localization Microscopy
Biophysical Journal. 2017. DOI : 10.1016/j.bpj.2017.09.032.DeconvolutionLab2: An Open-Source Software for Deconvolution Microscopy
Methods—Image Processing for Biologists. 2017. DOI : 10.1016/j.ymeth.2016.12.015.Pancreatic α- and β-Cellular Clocks Have Distinct Molecular Properties and Impact on Islet Hormone Secretion and Gene Expression
Genes & Development. 2017. DOI : 10.1101/gad.290379.116.Spline Shape Processing : Representation, Learning, and Modeling
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-8174.SpotCaliper: Fast Wavelet-Based Spot Detection with Accurate Size Estimation
Bioinformatics. 2016. DOI : 10.1093/bioinformatics/btv728.Transforms and Operators for Directional Bioimage Analysis: A Survey
Advances in Anatomy, Embryology and Cell Biology; Springer International Publishing, 2016.On the Continuous Steering of the Scale of Tight Wavelet Frames
SIAM Journal on Imaging Sciences. 2016. DOI : 10.1137/15M1033885.Variational Phase Imaging Using the Transport-of-Intensity Equation
IEEE Transactions on Image Processing. 2016. DOI : 10.1109/TIP.2015.2509249.A Feasability Study of Color Flow Doppler Vectorization for Automated Blood Flow Monitoring
Journal of Clinical Monitoring and Computing. 2016. DOI : 10.1007/s10877-016-9953-2.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. 2016. DOI : 10.1016/j.wear.2016.06.006.Super-Resolution Fight Club
Nature Photonics. 2016. DOI : 10.1038/nphoton.2016.22.Quantitative evaluation of software packages for single-molecule localization microscopy
Nature Methods. 2015. DOI : 10.1038/Nmeth.3442.Fast Detection and Refined Scale Estimation Using Complex Isotropic Wavelets
2015. p. 512 - 515. DOI : 10.1109/ISBI.2015.7163923.Analysis of S. pombe SIN protein association to the SPB reveals two genetically separable states of the SIN
Journal Of Cell Science. 2015. DOI : 10.1242/jcs.160150.Photobleaching Kinetics and Time-Integrated Emission of Fluorescent Probes in Cellular Membranes
Molecules. 2014. DOI : 10.3390/molecules190811096.Phase Retrieval by Using Transport-of-Intensity Equation and Differential Interference Contrast Microscopy
2014. p. 3939 - 3943. DOI : 10.1109/ICIP.2014.7025800.Autonomous and self-sustained circadian oscillators displayed in human islet cells
Diabetologia. 2013. DOI : 10.1007/s00125-012-2779-7.Circadian Clock Characteristics Are Altered in Human Thyroid Malignant Nodules
Journal Of Clinical Endocrinology & Metabolism. 2013. DOI : 10.1210/jc.2013-2568.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. 2013. DOI : 10.1186/1747-1028-8-6.3-D PSF fitting for fluorescence microscopy: implementation and localization application
Journal Of Microscopy. 2013. DOI : 10.1111/j.1365-2818.2012.03675.x.Advanced Image Processing for Biology, and the Open Bio Image Alliance (OBIA)
2013.Benchmarking Image-Processing Algorithms for Biomicroscopy: Reference Datasets and Perspectives
2013.Predicting stem cell fate changes by differential cell cycle progression patterns
Development. 2012. DOI : 10.1242/dev.086215.Bi-Exponential Edge-Preserving Smoother
Ieee Transactions On Image Processing. 2012. DOI : 10.1109/Tip.2012.2200903.Experimental investigation of collagen waviness and orientation in the arterial adventitia using confocal laser scanning microscopy
Biomechanics and Modeling in Mechanobiology. 2012. DOI : 10.1007/s10237-011-0325-z.A Psf-Based Approach To Biplane Calibration In 3D Super-Resolution Microscopy
2012. 9th IEEE International Symposium on Biomedical Imaging (ISBI) - From Nano to Macro. p. 1232 - 1235. DOI : 10.1109/ISBI.2012.6235784.Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation
Bmc Bioinformatics. 2012. DOI : 10.1186/1471-2105-13-296.Potential of Ultraviolet Wide-Field Imaging and Multiphoton Microscopy for Analysis of Dehydroergosterol in Cellular Membranes
Microscopy Research And Technique. 2011. DOI : 10.1002/jemt.20878.Fast O(1) Bilateral Filtering Using Trigonometric Range Kernels
IEEE Transactions on Image Processing. 2011. DOI : 10.1109/TIP.2011.2159234.Flow measurements in sewer systems based on image analysis: automatic flow velocity algorithm
Water Science and Technology. 2011. DOI : 10.2166/wst.2011.176.Multicolor Bleach-Rate Imaging Enlightens in vivo Sterol Transport
Communicative & Integrative Biology. 2010. DOI : 10.4161/cib.3.4.11972.Flow Measurements in Sewer Systems Based on Image Analysis: Automatic Flow Velocity Algorithm
2010. p. 180 - 189.Flow measurements in sewer systems based on image analysis: automatic flow velocity algorithm
2010. 7th International conference on sustainable techniques and strategies in urban water management (NOVATECH), Lyon, France, June 27 - July 1st, 2010.Comparison of Deconvolution Software: A User Point of View—Part 2
G.I.T. Imaging & Microscopy. 2010.Fast Detection of Cells Using a Continuously Scalable Mexican-Hat-Like Template
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.Comparison of Deconvolution Software in 3D Microscopy: A User Point of View—Part 1
G.I.T. Imaging & Microscopy. 2010.Low-Bond Axisymmetric Drop Shape Analysis for Surface Tension and Contact Angle Measurements of Sessile Drops
Colloids and Surfaces A: Physicochemical and Engineering Aspects. 2010. DOI : 10.1016/j.colsurfa.2010.04.040.Selective Visualization of Fluorescent Sterols in Caenorhabditis elegans by Bleach-Rate-Based Image Segmentation
Traffic. 2010. DOI : 10.1111/j.1600-0854.2010.01040.x.A software solution for recording circadian oscillator features in time-lapse live cell microscopy
Cell Division. 2010. DOI : 10.1186/1747-1028-5-17.Vision-based system for the control and measurement of wastewater flow rate in sewer systems
Water Science and Technology. 2009. DOI : 10.2166/wst.2009.659.Vision-Based System for the Control and Measurement of Wastewater Flow Rate in Sewer Systems
2009. p. OP03 - 4.Effect of aging on elastin functionality in human cerebral arteries
Stroke; a journal of cerebral circulation. 2009. DOI : 10.1161/STROKEAHA.108.528091.Circadian gene expression is resilient to large fluctuations in overall transcription rates
The EMBO journal. 2009. DOI : 10.1038/emboj.2008.262.Multiresolution Monogenic Signal Analysis Using the Riesz-Laplace Wavelet Transform
Ieee Transactions On Image Processing. 2009. DOI : 10.1109/TIP.2009.2027628.Phosphorylation does not prompt, nor prevent, the formation of alpha-synuclein toxic species in a rat model of Parkinson's disease
Human Molecular Genetics. 2009. DOI : 10.1093/hmg/ddn417.Effect of Ageing on Elastin Functionality in Human Cerebral Arteries
2008. ASME 2008 Summer Bioengineering Conference (SBC'08), Marco Island FL, USA, June 25–29, 2008. p. 959 - 960. DOI : 10.1115/SBC2008-192727.Selective visualization of fluorescent sterols in Caenorhabditis elegans
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.Controlled Exchange of Chromosomal Arms Reveals Principles Driving Telomere Interactions in Yeast
Genome Research. 2008. DOI : 10.1101/gr.6687808.The Marr Wavelet Pyramid and Multiscale Directional Image Analysis
2008.Coupled tomography and distinct-element-method approach to exploring the granular media microstructure in a jamming hourglass
Physical Review E. 2008. DOI : 10.1103/PhysRevE.77.061306.Lung Tissue Classification Using Wavelet Frames
2007. p. 6259 - 6262. DOI : 10.1109/IEMBS.2007.4353786.A Snake-Based Approach to Accurate Determination of Both Contact Points and Contact Angles
Colloids And Surfaces A: Physicochemical And Engineering Aspects. 2006. DOI : 10.1016/j.colsurfa.2006.03.008.IP-LAB: A Tool to Teach Image Processing Programming in Java—Challenge in Swiss Federal Institute of Technology Lausanne
2005. p. 473 - 474.Image Processing Education
Handbook of Image & Video Processing (Second Edition); Amsterdam, The Netherlands: Elsevier Academic Press, 2005. p. 73 - 95.Automatic Tracking of Individual Fluorescence Particles: Application to the Study of Chromosome Dynamics
IEEE Transactions on Image Processing. 2005. DOI : 10.1109/TIP.2005.852787.Analyse des caractéristiques géométriques d'amas granulaires réels et simulés
2005PixFRET, an ImageJ Plug-in for FRET Calculation That Can Accommodate Variations in Spectral Bleed-throughs
Microscopy Research and Technique. 2005. DOI : 10.1002/jemt.20215.Extended Depth-of-Field for Color Images in Light Microscopy: Image Fusion and 3D Visualization
Proceedings of the 2004 Annual Meeting of the Swiss Society of Biomedical Engineering (SSBE'04), Zürich, Switzerland, September 2-3, 2004.Extended Depth-of-Focus for Multi-Channel Microscopy Images: A Complex Wavelet Approach
2004. p. 660 - 663. DOI : 10.1109/ISBI.2004.1398624.Complex Wavelets for Extended Depth-of-Field: A New Method for the Fusion of Multichannel Microscopy Images
Microscopy Research and Technique. 2004. DOI : 10.1002/jemt.20092.Automatic Tracking of Particles in Dynamic Fluorescence Microscopy
2003. p. 582 - 586. DOI : 10.1109/ISPA.2003.1296963.Teaching Image-Processing Programming in Java
IEEE Signal Processing Magazine. 2003. DOI : 10.1109/MSP.2003.1253553.Easy Java Programming for Teaching Image Processing
2001. p. 298 - 301. DOI : 10.1109/ICIP.2001.958110.Teaching & PhD
Past EPFL PhD Students as codirector
Daniel Andreas Schmitter, Anaïs Badoual, Laurène Donati
Courses
Bioimage informatics
BIO-410
The course provides a comprehensive overview of methods, algorithms, and computer tools used in bioimage analysis. It exposes fundamental concepts and practical computer solutions to extract quantitative information from multidimensional images, both using engineering methods and deep learning.
Fundamentals of Image Analysis
EE-805
This summer school is an hands-on introduction on the fundamentals of image analysis for scientists. A series of lectures provide students with the key concepts in the field, and are followed by practical sessions with popular software on the participants' own image-analysis software.
Image processing II
MICRO-512
Study of advanced image processing; mathematical imaging. Development of image-processing software and prototyping in Jupyter Notebooks; application to real-world examples in industrial vision and biomedical imaging.