I also use a digital camera for chip images. I take the picture at high resolution, but at a distance (so the chip is in focus.) Typically, that means about 2-3" from the chip. Then I have to crop the image (I use LView Pro for this.)
As far as using a flash or not . . I always take several pictures for each one I use. So I will take images both with the flash on and off. I also like to shoot from different angles to try and cut down on the glare.
I think the best advise is to plan on taking several shots to generate the kind image you want. Change the parameters a little each time (flash, distance to object, point of view, exposure time or shutter speed.) As you gain experience, you will develop a very good feel for what seems to work best to give you the results you want.
Good luck!
(As you can see from the image below, I’m still learning!)
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