Useful links
General microscopy
- many of the basic concepts in microscopy are covered here -
http://micro.magnet.fsu.edu/primer/index.html
https://www.leica-microsystems.com/science-lab/
http://zeiss-campus.magnet.fsu.edu/
https://www.ibiology.org/online-biology-courses/microscopy-series/ (video lectures covering many aspects of basic and advanced microscopy)
- lectures on bioimage analysis
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
http://www.fpvis.org/FP.html (constitutively fluorescent proteins)
http://www.fpvis.org/PSFP.html (photochromic fluorescent proteins)
- an almost comprehensive database of many fluorescent proteins, their sequences, 1 and 2p spectra etc.
https://www.fpbase.org/ (find all about your fluorescent protein)
https://www.fpbase.org/spectra/ (spectra viewer)
https://www.fpbase.org/fret/ (FRET pairs and FRET parameters)
- a very nice spectra viewer by Stephan Junek and his group from Max Planck Institute for Brain Research in Frankfurt, Germany
Image analysis
Fiji (powerful open-source image analysis software - “Swiss Army knife” of bioimage analysis)
Napari (an open-source, Python-based image viewer designed for n-dimensional data)
CellProfiler (a free, open-source software designed for quantitative analysis of microscopy data)
ilastik (a free, open-source tool for interactive, AI-based, image segmentation that makes machine learning accessible to non-programmers)
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)
Icy (free, open-source platform for bioimage analysis)
BISE (database and search engine of bioimage analysis tools, programs, plugins etc.)
Image.sc (a forum where questions about the usage of most major image data handling software can be asked)
Github page of IDIP (https://github.com.mcas.ms/IDIP-Platform) where one can find image analysis workflows from our collaboration projects
Others
GermanBioImaging (network of microscopists and imaging specialists, contains useful links, events, teaching material)
NEUBIAS (network of bioimage analysts, contains bioimage analysis related events, career and grants information)