MPI Martinsried (3-day) * I am (your position) Undergraduate student PhD student PostDoc Facility Manager Reserach group leader (PD, Prof.) Technician * I will use the following computer system during the course: Windows (PC) MAC (OSX) Linux (might not be fully functional) * I am doing imaging experiments… make a selection…3x per week or more frequent2x per week1x per week3x per month2x per month1x per month7-11x per year4-6x per year1-3x per yearno imaging experience * I consider my experience level with scientific images as… very basic (need to learn about image handling and want to see basic analysis methods) basic (I worked with images but want to have info on image handling as well as different processing and analysis methods) intermediate (some info on basics are ok and then I’m interested in advanced processing and analysis methods) experienced (I know all about correct image handling, I am more interested in advanced processing and analsis methods) * So far, I was using some of the following programs to process/analyze my images I did not analyze images so far Fiji ImageJ Adobe Photoshop Gimp BioimageXD / ICY CellProfiler Matlab Imaris / Volocity other * I am doing research in the following areas: shortly describe if you are working with a specific imaging devices and which kind of samples (cells, animal, human patients,…) and shortly mention imaging related methods you are working with (e.g. confocal, brightfield, IF, ICC, IHC, tracking, co-localization,………) * I am interested in topics regarding the following specific image processing or analysis (multiple selection possible). Due to time reasons we need to restrict to the topics interesting for the majority of the participants. Important considerations for basic image adjustments (contrast, image rotation and size adjustments) Background correction methods (including unequal lighting correction) Extracting specific objects from intensity-based (fluorescence) image (image filtering and segmentation) Analysis of histological sections and stainings (from chemical IHC stainings) Automated counting of specific objects (cells, particles,…) 2D measurements (area, length, shape,…) Correct intensity quantification of fluorescent images First steps in ImageJ/Fiji macro recording for individual processing and analysis automation Do’s and Dont’s of publication figure preparation No specific analysis interest / want to get an overview * For the remaining time we will talk about additional optional analysis methods. Please choose one of the following which seems most important/interesting for your work. Highest voting decides about the method we will include. Besides this we also might include time for individual solutions. Optional part 1 Basics in manual macro scripting for customized automation (manually adjust recorded macros) Statistical co-localization analysis (of objects from different fluorescent channels) I would prefer to work on my own images under supervision in the remaining time to practice the learned * Optional part 2 Detailed automated tracking and analysis of moving objects in 4D 3D Network Tracing (analyzing neuronal networks or vessels in 3D space) 3D-Segmentation (extracting features/objects from 3D images, e.g. tumors in medical MRI-stacks) and 3D measurements (volume, surface, intensity, object distances) I would prefer to work on my own images under supervision in the remaining time to practice the learned Basics in manual macro scripting for customized automation (manually adjust recorded macros) Advanced Macro Programming (based on basics from option above) * I have the following question or problen when analyzing or preparing my scientific images (best send an example by mail beforehand)
