Digital image processing/analysis tools in Light Microscopy: From the basics and beyond
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1 Regional course Addressed to Balkan, SE Mediterranean and N. African countries Digital image processing/analysis tools in Light Microscopy: From the basics and beyond 1 st Day, Monday, June 10 PROGRAM Image analysis - history and present/open source software for bio imaging 8:30-9:00 Registration 9:00-9:10 Welcome-opening remarks: Haralabia Boleti, Light Microscopy unit, Hellenic Pasteur Institute 9:10-10:00 Stamatis Pagakis, Biomedical Research Foundation Academy of Athens A historical perspective to digital Image analysis and its applications to biomedical sciences. Extraction of quantitative information from digital images. 10:00-11:00 Jean Christophe Olivo Marin, Institut Pasteur, Paris, France Image analysis and computer vision tools for the processing and quantification of biological images. Icy the open source computer software for bio imaging. 11:30 12:30 Pavel Tomancak, Max Plank Institute, Dresden Germany Open source bioimage Informatics 12:30-13:30 Lunch break 13:30-14:00 Pavel Tomancak: Introduction to ImageJ/Fiji 14:00-19:00 ImageJ/Fiji free software, hands on practical session Quantitative Morphometric analysis, image & video editing Instructors : Pavel Tomancak, Tobias Pietzsch, F.Frischnecht 2 nd Day, Tuesday June 11 Imaging in Infectiology quantitation of dynamic processes 1
2 8:30-9:30 Freddy Frischnecht, U. of Heidelberg Medical School, Germany Malaria parasite migration Dynamics of Plasmodium motility in vitro and in vivo. 9:30-10:30 Javier Pizarro-Cerda, Institut Pasteur, France Analyzing invasion of host cells by the bacterial pathogen Listeria monocytogenes. 10:30-11:00 Coffee break 11:00 12:00 Isabelle Tardieux, Institut Cochin, France The use of correlative fluorescence microscopy and EM tomography as well as speckle fluorescence microscopy to elucidate the role of toxofilin during Toxoplasma gondii entry into host cells. 12:00-13:00 Haralabia Boleti, Hellenic Pasteur Institute, Greece Leishmania phagocytosis in macrophages. Dynamics of the parasitophorous vacuole maturation. 13:00-14:00 Lunch break 14:00-14:30 Jean Christophe Olivo: introduction to Icy practical session 14:30-19:00 Icy free software Instructors: Fabrice de Chaumont, Alexandre Dufour, Stephane Dallongeville 3 rd Day, Wednesday June 12 Image analysis in Cell Biology, super resolution and spectral imaging 9:00-9:30 Maria Evagelidou, Hellenic Pasteur Institute, Greece Ratiometric imaging of Ca++ signaling in neurons. 9:30-10:00 Maria Gaitanou, Hellenic Pasteur Institute, Greece Subcellular localization and targeting in the mitochondria of the neuronal protein Cend1. Colocalization analysis. 10:00-11:00 Ricardo Henriques, Institut Pasteur, France Easy cell super-resolution imaging and analysis with ImageJ and other free tools 11:30-12:30 Costas Balas, Technical University of Crete, Greece Dynamic and Spectral Imaging: system design, hardware configurations and applications in in vivo and in vitro microscopy. 12:30-14:00 Lunch break 2
3 13:30-16:00 Cell profiler Instructor: Javier Pizzaro Cerda Quantitative measurement of phenotypes from thousands of images automatically 16:00-19:00 Informal tutorials with the instructors Practice on Icy, Fiji/ ImageJ & Cell Profiler Instructors: Fabrice de Chaumont, Alexandre Dufour, Stephane Dallongeville Freddy Frischnecht, Ricardo Henriques, JavierPizzaro-Cerda, Tobias Pietzsch Evangelia Xingi 4 rth Day, Thursday June 13 Thick tissue imaging and cell tracking in neuroscience & stem cell biology 9:00-10:00 Igor Adameyko, Karolinska Institute, Sweeden Practical approaches to 3-D imaging and reconstruction of the whole mount stained E8-E12 mouse embryos and large fragments of tissue. 10:00-11:00 Dimitra Thomaidou, Hellenic Pasteur Institute, Greece Reprogramed astrocytes into the injured mouse brain: analysis of their proliferation and differentiation properties using lineage tree and co- localization analysis. 11:30-12:30 Felipe Ortega, Institute of Physiology, Ludwig-Maximilians Univ.,Germany Long term single cell imaging of Stem Cells using "TTT" (Timm's Tracking Tool) software. 12:30-13:30 Lunch break 13:30-18:30 TTT (Timm's Tracking Tool) Instructors: Felipe Ortega, Katerina Aravantinou-Fatorou, Evangelia Xingi division cell tracking, measurement of cell cycle length, number of divisions, genealogic lineage trees drawing 5 th Day, Friday June 14 Commercial packages for 3D reconstruction, object segmentation & deconvolution 8:45-9:45 Delisa Ibanez Garcia, Bitplane AG, Imaris: at the cutting edge of 3D and 4D image visualization and analysis 9:45-10:45 Vincent Schoonderwoert, Scientific Volume Imaging, The Netherlands Improving 3D image resolution, signal to noise and analysis with Huygens deconvolution. 10:45-11:15 Evangelia Xingi, Hellenic Pasteur Institute, Greece Digital image processing: analysis tools used in the HPI Light Microscopy Unit 11:15-11:30 Coffee break 3
4 Practical session hands on training on computational algorithms 11:30-13:30 Bitplane/Imaris 13:30-14:30 Lunch break Practical session hands on training on computational algorithms 14:30-17:30 19:00-24:00 Cultural and social event 19:00-21:00 Guided tour to the New Acropolis museum 21:00-23:30 Dinner at the restaurant of the Acropolis museum 6 th Day, Saturday June 15 Practical session hands on training on computational algorithms 9:30-13:00 13:00 14:00 Lunch break 14:00 16:30 16:30-17:00 Coffee break 17:00-19:00 Informal tutorials Practice on any of the 5 software (Icy, ImagJ/Fiji, Imaris Cell, SVI and TTT) with the help of instructors 4
5 7 th Day, Sunday June 16 9:00-21:00 Cultural and social event One day excursion to the island of Aegina and to the archaeological site of Aphaia Temple 8 th Day, Monday June 17 9:00-13:30 Tutorials and practice Participants will work on their projects on the different software they have been trained during the course with the assistance of instructors and will prepare their presentations. 13:30 14:30 Lunch break 14:30 18:00 Student Presentations Students will present the results from their course projects in 10 min presentations. 18:00 18:30 END of course closing remarks 5
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