[Microbiology] Photographing bacteria in a Gram's stain

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Hi can anyone share tips and tricks on capturing images of bacteria stained 
by Gram's method.
I'm using an Olympus BX51 with a DP70 and capturing the images using Olysia 
BioReport.
While I'm finding the process excellent for larger organisms via a 40 
objective, when using oil 100 focusing and sharpness have suffered.
Everything looks good on the screen, but then I transfer the image (saved as 
tif and usually around 36 MB) and attempt some manipulation with Photoshop 
to resize to 96 dpi and save as jpg (10/10 quality) the picture degrades a 
little.
Thanks in advance. I'm mostly keen to get any help on the best focussing 
techniques people use.