Useful Links

Useful resources including methods, technical development references, software downloads and software guides are available to all CBIA Core members through the CBIA Core Network drive “Demo” folder. Additional online resources on microscopy and analysis basics are linked here. Please feel free to contact us with useful resources you have found to share with others.

General References

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:

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


Interesting articles

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 fluorescent proteins


Reproducibility and Metadata


Key Concepts

Numerical Aperture and resolution


Spectral Databases

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.



Chroma Spectra Viewer


Antibody Database

Antibody database based on published scientific articles

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


Open Source Software/Freeware

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.

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