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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.

FluorPlan Spectra Viewer from eBioscience (Java required).

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 Image J is the Image J homepage of the Wright Cell Imaging Facility, as well as the searchable archives of the ImageJ Listserv and the ImageJ Information and Documentation Portal.

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. An older version of Zeiss LSM Image browser (2.8), which is also compatible with the images from the SP2microscope, is available for direct download here (2.1MB; right mouse click).

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