Useful links

Over the last several years there has been an explosion of educational websites with a focus on microscopy. Some of the most useful sites are listed below:

• Up to date ressources (jobs, events, education tools) on Focal Plane
• ELMI 2022 videos
• Sample preparations and dyes- A great sample preparation resource for techniques, applications and dyes for many needs. 
• Molecular Expressions Optical Microscopy Primer- a great microscopy resource which discusses many aspects of microscopy in an understandable fashion. Their virtual microscopes are informative as well as fun.
• Zeiss Campus- The Carl Zeiss Microscopy Online Campus website explores the fascinating world of optical microscopy and provides the necessary background to understand both the basic concepts and advanced principles.
• Olympus Microscopy Resource Center- includes a microscopy primer as well as information about general microscopy, confocal microscopy, digital imaging, and advanced techniques.
• Nikon MicroscopyU - Another useful resource for information on confocal as well as general microscopy.
• MyScope-training for advanced research - Useful resource for information on confocal as well as general microscopy, with a final quiz to test your microscopy knowledge
• Quantifying Microscopy Images: 10 Tips for Image acquisition - a Quick summary of what you should do and don't. Because with the "power of Microscopy comes Responsability and no amount of fancy image analysis can overcome image acquisition problems" Prof. Anne Carpenter

• Colour me better: fixing figures for colour blindness
• Publishers unite to tackle doctored images in research papers and Check the guide about Image integrity
• Creating Clear and Informative Image-based Figures for Scientific Publications
• Effective image vizualization for publications
• Tutorial: guidance for quantitative confocal microscopy
• Sharper signals: how machine learning is cleaning up microscopy images
• The hunt for red fluorescet proteins
• Reproducibility
• Reproducibility and Metadata

• Numerical Aperture and resolution

Below are some useful sites containing fluorophore excitation/emission spectra databases. These are great resources to assess the spectral separation and bleed through of your fluorophores before carrying out your experiments. You can also use these resources to view spectra and compare your fluorophore options to the filter sets which are available on the microscopes within the core facility.

• FPbase
• Spectraviewer
• Chroma Spectra Viewer

Antibody database based on published scientific articles

Database Improving the integrity and reproducibility of research that uses antibodies. The paper

Nature article: "When antibodies mislead: the quest for validation".

• Fiji- a useful image processing program derived from ImageJ, with many plugins already included. To give you a good start you can read this book from Dr Bankhead: Analyzing fluorescence microscopy images with ImageJ
• CellProfiler and CellProfiler Analyst- open source HCS image analysis software available from the Broad Institute.