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Links of Interest

Microscopy and Image Analysis

General References

There are a number of educational websites with a focus on microscopy. Some of the most useful sites are listed below:

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.

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.

Microscopy Alliance - Extensive index from the University of Arizona Experimental Pathology Service Core, which contains an index for Confocal Microscopy.

Archives of the Confocal Listserver - Searchable archives from the Confocal e-mail user's group.

Assay Guidance Manual - eBook from the NCBI which covers development of assays for HCS/HTS, but also useful for smaller scale assays.


Some useful sites containing fluorophore excitation/emission spectra databases are:

Spectraviewer from Thermo Fisher (formerly Molecular Probes).

Fluorescence Spectrum Viewer from Becton Dickinson.

Fluorescent Protein Resource Center - in addition to excitation/emission maxima it contains other useful information about fluorescent proteins and their properties.

Open Source Software / Freeware

ImageJ -Sophisticated Java-based freeware program which is able to run on any platform and is available from the National Institutes of Health allowing post-acquisition processing and analysis of confocal images, image stacks and much more. A good site with tips for how to get started using ImageJ is the homepage of the ImageJ, as well as the searchable archives of the ImageJ Listserv.

Fiji - a useful image processing program derived from ImageJ, with many microscopy plugins already included.

NIH Image - the original Macintosh-based version of the program. The NIH-Image in Fluorescence and Confocal Microscopy manual can help you get started.

CellProfiler and CellProfiler Analyst - open source HCS image analysis software available from the Broad Institute.

Company Sites

Carl Zeiss website - where you can download an offline version of ZEN lite software, a useful Windows-based freeware program you can use to help with examination of confocal images. 

Olympus Deutschland - where you can get more information about the Scan^R Screening Station.

Leica Microsystems - where you can get more information about the Leica spectral confocal microscopes.

Linscott's Directory - Directory of commercially available antibodies.

Antikoerper Online - Directory of commercially available antibodies