Useful links
General microscopy
- many of the basic concepts in microscopy are covered here -
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http://micro.magnet.fsu.edu/primer/index.html
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https://www.leica-microsystems.com/science-lab/
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http://zeiss-campus.magnet.fsu.edu/
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https://www.ibiology.org/online-biology-courses/microscopy-series/ (video lectures covering many aspects of basic and advanced microscopy)
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- lectures on bioimage analysis
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Lectures by Robert Haase, Lecturer and Training Coordinator, Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Leipzig University on basics of bioimage analysis using different software​
Fluorophores and their properties
- interactive database of many common fluorescent proteins, their properties and associated literature
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http://www.fpvis.org/FP.html (constitutively fluorescent proteins)
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http://www.fpvis.org/PSFP.html (photochromic fluorescent proteins)
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- an almost comprehensive database of many fluorescent proteins, their sequences, 1 and 2p spectra etc.
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https://www.fpbase.org/ (find all about your fluorescent protein)
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https://www.fpbase.org/spectra/ (spectra viewer)
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https://www.fpbase.org/fret/ (FRET pairs and FRET parameters)
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- a very nice spectra viewer by Stephan Junek and his group from Max Planck Institute for Brain Research in Frankfurt, Germany
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Image analysis
Fiji (powerful open-source image analysis software - “Swiss Army knife” of bioimage analysis)
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Napari (an open-source, Python-based image viewer designed for n-dimensional data)
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CellProfiler (a free, open-source software designed for quantitative analysis of microscopy data)
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ilastik (a free, open-source tool for interactive, AI-based, image segmentation that makes machine learning accessible to non-programmers)
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QuPath (a free, open-source software platform for image analysis especially useful when dealing with very large images (whole slide scans) or highly multiplexed images)
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Icy (free, open-source platform for bioimage analysis)
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BISE (database and search engine of bioimage analysis tools, programs, plugins etc.)
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Image.sc (a forum where questions about the usage of most major image data handling software can be asked)
Others
GermanBioImaging (network of microscopists and imaging specialists, contains useful links, events, teaching material)
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NEUBIAS (network of bioimage analysts, contains bioimage analysis related events, career and grants information)