Fluorescent microscopy: There is one light source and then there are set of filters such as DAPI, GFP, YFP, RFP,etc. attached to the microscope to see the fluorescence. Image resolution may not be optimal as you see all possible light coming from your sample which is specific for that filter i.e. light is coming from the area which is not in focus. But is a good way of screening your sample.
Confocal microscope: Light source is Laser light. For DAPI it is usually 405 diode (UV light) as the stain is excited at 405nm wavelength. For GFP the excitation is 488nm and for YFP it is 514nm. Confocal gives better resolution images as it eliminates all the out of focus light. So you only see the images that are in focus (it is also called optical sectioning). This will be better for Chromosome counting as the resolution will be better.
If you want a good imaging of chromosomes with both conventional fluorescence microscopes, semi-confocal technologies and/or confocal microscopes (even super-resolution and nanoscopy microscopes) then forget about DAPI mounting medium, specially Vectas..... this will cause an high background, diffused two-photons emission that will coock your samples and inefficiency in your overall imaging. I'd like to suggest you to use Hoechst 33342 or picogreen for DNA visualization (compatibly with other fluorocromes you need in your preps), stain, wash, rinse and mount with a DAPI-free mounting medium. Optical index is something unknown by most but really important for imaging. Your mounting medium OI should match those of your coverslip and immersol (immersion oil) if used. Glycerol is really good (90% glycerol with clean PBS is fine). Antifading and antiquencing is extremely important to me so bear in mind that. Other commercial mounting medium are extremely well made in that sense. Also Mowiol powder could be used to make an excellent mounting medium but as well as glycerol you must add an antifading at least. Always clean coverslips and never autoclave them, they're not pirex glass and they'll be coocked.
feel free to ask any other question.
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