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
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STI
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IEM
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LIB
Web site: Web site: https://bigwww.epfl.ch/
+41 21 693 91 32
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SSV-ENS
Web site: Web site: https://sv.epfl.ch/education
+41 21 693 91 32
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EPFL IMAGING
BM 4142 (Bâtiment BM)
Station 17
1015 Lausanne
+41 21 693 91 32
Office:
BM 4135
EPFL
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VPA-AVP-CP
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IMAGING
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Fields of expertise
Publications
Publications
Coordinates
Biomedical Imaging Group| 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 |
| daniel.sage@epfl.ch | |
| Web page | http://bigwww.epfl.ch/sage/ |
| Office | BM 4.135 |
Publications
Infoscience publications
Infoscience
JDLL: a library to run deep learning models on Java bioimage informatics platforms
Nature Methods. 2024-01-08. DOI : 10.1038/s41592-023-02129-x.A framework for evaluating the performance of SMLM cluster analysis algorithms
Nature Methods. 2023-02-01. DOI : 10.1038/s41592-022-01750-6.Correction of multiple-blinking artifacts in photoactivated localization microscopy
Nature Methods. 2022-05-11. DOI : 10.1038/s41592-022-01463-w.Steer'n'Detect: fast 2D template detection with accurate orientation estimation
Bioinformatics. 2022-04-18. DOI : 10.1093/bioinformatics/btac270.A Practical Guide to Supervised Deep Learning for Bioimage Analysis: Challenges and good practices
Ieee Signal Processing Magazine. 2022-03-01. DOI : 10.1109/MSP.2021.3123589.DeepImageJ: A user-friendly environment to run deep learning models in ImageJ
Nature Methods. 2021-09-30. 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. 2021-05-17. DOI : 10.1007/s10911-021-09485-4.Optimal-Transport-Based Metric for SMLM
2021-04-13. 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
2021-01-01. 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. 2020-02-04. DOI : 10.1073/pnas.1916539117.Reconstruction Methods for Cryo-Electron Microscopy: From Model-based to Data-driven
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7540.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.Pocket guide to solve inverse problems with GlobalBioIm
Inverse Problems. 2019-10-01. DOI : 10.1088/1361-6420/ab2ae9.Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software
Nature Methods. 2019-05-01. DOI : 10.1038/s41592-019-0364-4.Deforming Tessellations for the Segmentation of Cell Aggregates
2019-04-08. 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.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.SUBDIVIDE AND CONQUER Active Contours and Surfaces for Biomedical Image Segmentation
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9326.Achieving high-resolution thermal imagery in low-contrast lake surface waters by aerial remote sensing and image registration
Remote Sensing of Environment. 2019. DOI : 10.1016/j.rse.2018.12.018.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.Investigating Focal Adhesion Substructures by Localization Microscopy
Biophysical Journal. 2017. DOI : 10.1016/j.bpj.2017.09.032.Spline Shape Processing
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-8174.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.Parametric Experimental Study and Design of Experiment Modelling of Sapphire Grinding
Journal of Cleaner Production. 2017. DOI : 10.1016/j.jclepro.2016.09.031.Transforms and Operators for Directional Bioimage Analysis: A Survey
Advances in Anatomy, Embryology and Cell Biology; Springer International Publishing, 2016.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.On the Continuous Steering of the Scale of Tight Wavelet Frames
SIAM Journal on Imaging Sciences. 2016. DOI : 10.1137/15M1033885.SpotCaliper: Fast Wavelet-Based Spot Detection with Accurate Size Estimation
Bioinformatics. 2016. DOI : 10.1093/bioinformatics/btv728.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.Frequency fluctuations in silicon nanoresonators
Nature Nanotechnology. 2016. DOI : 10.1038/Nnano.2016.19.Super-Resolution Fight Club
Nature Photonics. 2016. DOI : 10.1038/nphoton.2016.22.Variational Phase Imaging Using the Transport-of-Intensity Equation
IEEE Transactions on Image Processing. 2016. DOI : 10.1109/TIP.2015.2509249.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.Phase Retrieval by Using Transport-of-Intensity Equation and Differential Interference Contrast Microscopy
2014. p. 3939-3943. DOI : 10.1109/ICIP.2014.7025800.Toward a Materials Genome Approach for Ionic Liquids: Synthesis Guided by Ab Initio Property Maps
Journal Of Physical Chemistry B. 2014. DOI : 10.1021/jp506972w.Photobleaching Kinetics and Time-Integrated Emission of Fluorescent Probes in Cellular Membranes
Molecules. 2014. DOI : 10.3390/molecules190811096.Benchmarking Image-Processing Algorithms for Biomicroscopy: Reference Datasets and Perspectives
2013.Advanced Image Processing for Biology, and the Open Bio Image Alliance (OBIA)
2013.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.Autonomous and self-sustained circadian oscillators displayed in human islet cells
Diabetologia. 2013. DOI : 10.1007/s00125-012-2779-7.Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation
Bmc Bioinformatics. 2012. DOI : 10.1186/1471-2105-13-296.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.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.Predicting stem cell fate changes by differential cell cycle progression patterns
Development. 2012. DOI : 10.1242/dev.086215.Fast O(1) Bilateral Filtering Using Trigonometric Range Kernels
Ieee Transactions On Image Processing. 2011. DOI : 10.1109/TIP.2011.2159234.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.Flow measurements in sewer systems based on image analysis: automatic flow velocity algorithm
Water Science and Technology. 2011. DOI : 10.2166/wst.2011.176.Flow Measurements in Sewer Systems Based on Image Analysis: Automatic Flow Velocity Algorithm
2010. p. 180-189.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.A software solution for recording circadian oscillator features in time-lapse live cell microscopy
Cell Division. 2010. DOI : 10.1186/1747-1028-5-17.Influence des Etats-Unis dans les pays d'Amérique Latine
2010Comparison of Deconvolution Software: A User Point of View—Part 2
G.I.T. Imaging & Microscopy. 2010.Multicolor Bleach-Rate Imaging Enlightens in vivo Sterol Transport
Communicative & Integrative Biology. 2010. DOI : 10.4161/cib.3.4.11972.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.Comparison of Deconvolution Software in 3D Microscopy: A User Point of View—Part 1
G.I.T. Imaging & Microscopy. 2010.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.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. p. 180.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.Multiresolution Monogenic Signal Analysis Using the Riesz-Laplace Wavelet Transform
Ieee Transactions On Image Processing. 2009. DOI : 10.1109/TIP.2009.2027628.Circadian gene expression is resilient to large fluctuations in overall transcription rates
The EMBO journal. 2009. DOI : 10.1038/emboj.2008.262.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.HydroPix: A vision-based tool for the control of hydraulic structures in sewer systems
European Geoscience Union conference, Vienna, Austria, April 19-24.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.The Marr Wavelet Pyramid and Multiscale Directional Image Analysis
2008.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.Measurement of the surface water velocity based on video images.
2008Coupled 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.Controlled Exchange of Chromosomal Arms Reveals Principles Driving Telomere Interactions in Yeast
Genome Research. 2008. DOI : 10.1101/gr.6687808.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.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.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.Image Processing Education
Handbook of Image & Video Processing (Second Edition); Amsterdam, The Netherlands: Elsevier Academic Press, 2005. p. 73-95.Extended Depth-of-Focus for Multi-Channel Microscopy Images: A Complex Wavelet Approach
2004. p. 660-663. DOI : 10.1109/ISBI.2004.1398624.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.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.Conditional mutation of Rb causes cell cycle defects without apoptosis in the central nervous system
Molecular and Cellular Biology. 2003. DOI : 10.1128/MCB.23.3.1044-1053.2003.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
Courses
Fundamentals of Image Analysis
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
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.