The following softwares are extremely useful for the analysis and processing of images captured on our instruments. Both of these softwares are installed on the Image Analysis Station at the CMCI.
FIJI (Fiji Is Just ImageJ) is a "batteries included" version of ImageJ that is highly-flexible, programmable, and free. It can open nearly every image format, including the proprietary formats favoured by each microscope manufacturor. http://fiji.sc
IMARIS is an extremely powerful software tool for the analysis of multidimensional fluorescent datasets. It has been designed with cell biology in mind, and can be used to track and measure cells and subcellular compartments over time. http://www.bitplane.com/
The following links are excellent resources for learning the underlying principles of light microscopy.
Nikon Microscopy : http://www.microscopyu.com/
Scientific Volume Imaging : http://www.svi.nl/FrontPage
Canadian Cytometry & Microscopy Association : http://cytometry.ca
Education in Microscopy and Digital Imaging : http://zeiss-campus.magnet.fsu.edu
If you prefer to learn visually, iBiology.org hosts an excellent series of youtube videos delivered by experts in that explain thoroughly all of the fundamental and advanced principles of light microscopy. You can find these videos by following this link: https://www.ibiology.org/ibioeducation/taking-courses/ibiology-microscopy-course.html
The confocal listserv is an international mailing list that is populated by experts in all fields of microscopy; if you have a question about any aspect of microscopy that our staff cannot answer, this is an excellent resource. http://confocal-microscopy-list.588098.n2.nabble.com/