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SUMMARY:Basic Microscopic Image Processing and Analysis
DESCRIPTION:Detailed workinar content overview: \n\nShort Introduction to Fiji / ImageJ and basic functions\nOverview over proper scientific image file formats\, metadata\, bit depth\nIn-depth practical introduction to pre-processing\n\nAutomatic uneven lighting correction\nUnderstanding of image filters and their use cases for improved object detection\nAutomatic background subtraction algorithms to reduce unspecific signal\n\n\nObject segmentation with automatic intensity thresholds (semantic segmentation)\nIndividual object labeling (instance segmentation)\nBasic insight into some user friendly machine learning plugins in comparison to classical segmentation\nOptimization of segmentation with post-processing methods\nQuality control of segmentation results\nDifferent basic automatic analyses (object counting\, measurements\, shapes\, intensities)\nOptional dependent on time: How to deal with 3D data in image analysis\nShort introduction to macro recording for automation.\n\n\n\nAll methods are learned hands-on with plenty of practical exercises to get confidence in applying them in your daily work. \nCategory: \nGSP / Data Analysis / Hard Skills \nVenue: \nThe workshop will be held as a virtual live workinar with many hands-on sessions via Zoom. \nDuration: \n2 days\, each day 9:00 to ~15:30 (max\, mostly 15:00 but plan some buffer time) \nMain Target Group and Focus: \n\nLife or Natural Scientists starting PhD-student level (1st year) and above.\nOptimally\, some practical imaging experience is an advantage.\nOptimally\, you have visited the first BioVoxxel Workshop Scientific Image Editing and Figure Creation and have some prior knowledge on proper scientific image handling\, metadata\, the image histogram\, …\n\nThe course has a very strong focus on fluorescent micrographs! There will be NO analysis of gels or Western blots. Images from immunohistochemical stainings (non-fluorescent) will also be partially discussed\, since processing is in parts similar. \nDifficulty Level: \nThe difficulty level is medium and easy to follow in step by step procedures and in-depth explanation of the necessary background to the individual methods. Also scientists with some prior knowledge will still benefit from the methods taught. \nPre-requisites: \n\nThis workshop builds up on some basic knowledge from Scientific Image Editing and Figure Creation but can be done independently\nComputer or Laptop (PC or Mac; supported operating systems: Windows\, MacOS and Linux)\nStable internet connection\nMouse and Headset/Microphone\nOptimally a webcam\nBest 2 monitors to watch the workinar on one and do the practical part on the other.\nProficiency in handling your computer in general\nPossibility to install software on your computer (or administrator rights)\n\nSoftware: \nDuring the course we will exclusively work with a customized version of Fiji (ImageJ bundle) Fiji is free of charge\, accessible for everybody and open source. Prior software knowledge is not required but might be of advantage. \nRegistered participants will receive all information regarding software preparation on time before the workshop via email.
URL:https://cpi-online.de/workshop/basic-microscopic-image-processing-and-analysis/
LOCATION:Zoom
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