So if I was doing this in Photoshop, here's what I would do:

1. Select the Elliptical marquee tool by right-clicking the Quick Select tool in the left menu, then selecting Elliptical Marquee.

2. In the marquee bar that appears, you can select "Fixed size" or "Fixed ratio". It sounds like you want "Fixed size", to set how many pixels high and wide. You can also leave it as "Normal" and hold the shift key while you drag to select a perfect circle, as opposed to an oval or whatever.

3. There's no way to quickly save a selected area as a picture, so crop it, export the image, then do an undo (ctrl+z) to get back to the full original image.

4. Repeat.

BTW, if you have a high quality digital camera, it honestly works just as well as a scanner and you can probably fit more chips - they take photos as such a high resolution you won't be limited by the size of the scanner bed.

Let me know if this works; if not I can walk you through it in more detail.