My previous advisor used to joke that all you need to do microbiology is a sterile wooden stick. You can use this simple tool too isolate colonies, pick colonies, inoculate media and isolate DNA*. If you were to visit my bench, you would find a bucket of sterile sticks as I use them almost every day. However, I need a lot more than a wooden stick to get my research done. The machines I use most often are the thermocycler, FPLC, biacore and any kind of spectrophotometer. Unfortunately, my favorite tool, the microscope, is one I rarely use.
One of the major reasons I love this instrument because it enables me to actually see the microbes I am studying. Since my work typically involves using RNA, DNA or protein, I spend most of my time looking at tubes containing a clear solution, or a if I'm lucky, a solution containing a dye. If not a tube, then I'm probably viewing a stained gel (acrylamide or agarose). It's just not as visually stimulating as looking at something under the microscope.**
Another reason I like to use the microscope is because you can take pictures or video of what you observe. Pictures and videos typically go over really well in a seminar and when applicable, they are great in a paper. The presence of images or video in a paper was often a deciding factor when I was deciding on a paper for journal club. I think everyone agrees that it's nice to see something besides a graph or table every now and then.***
For researchers like me, there just isn't usually a reason to have photos or video from a microscope. However, when I can, I choose assays that utilize a microscope. For example, to assess translation, I'll use a reporter gene like GFP so that not only do I get to use the microscope, but I get to look at fluorescence and that is way cool. I've also used fluorescence to assess protein-protein interactions. In both of these cases I can use the microscope for qualitative "yes or no"-type of data and then if need be, I can use a fluorometer for more quantitative data.
To illustrate my point, here are images from wikimedia commons. I wanted to include videos, but blogger wasn't cooperating.****
*Once the DNA is precipitated, you can wind it around a sterile stick or toothpick in leu of centrifugation. This is not really effective if you aren't isolating a large quantity of DNA.
** Yes, you can visualize your data in ways that don't involve a microscope and as a general rule it's awesome to obtain data, be that data in the form of a band, a sensogram or absorbance reading, but in my opinion seeing your data in a living organism is way cool.
***Not that anything is wrong with a table or graph. Pretty much all my data is presented in this form.
****I know that there are many compelling images and videos utilizing fluorescence microscopy, but I am not sure what the rules are regarding image and video usage from scientific papers. If anyone would like to enlighten me, please feel free. If anyone knows of some better images, that I can post without committing any kind of offense or spending money, please let me know and I will be happy to post them.