I have not scanned glass negatives, but this is what I would do based on scanning ordinary film.

With the flatbed (with transparency adapter): Emulsion down, lifted off the scanner bed with sheets of paper or card stock. Look at existing film carriers for your scanner for an idea of how far the image has to be from the scan bed. The space is needed because the scanner is focused slightly above the glass plate. Emulsion up won't work because the thickness of the glass will hold the image above the scanner's DOF.

With an interchangeable lens camera: I would prefer using a mirrorless over a DSLR because mirrorless cameras have focusing aids, like magnification and focus peaking. Some newer DSLRs might have similar features or custom firmware (Magic Lantern) to add them.

• Use a macro lens. This is needed for the flat field.

• Set the negative holder far in front of a reflector, white wall, or soft box. Set up a flash unit with remote trigger. Imperfections in the reflector will show up in the image if the negative is too close.

  While you can use ambient lighting with longer exposures, the quality of light from flash is significantly better. Flash also eliminates any effect camera shake might have.

• Set the camera parallel to the negative holder. Put a mirror in the negative holder and center the lens view of itself in the mirror. Then lock everything down so nothing moves. Replace the mirror with the negative. Depending on your camera, you may have to turn image stabilization off.

• With aperture wide open, focus on the grain. Hard light at an angle can make grain easier to see.

• Shield the area around the negative to prevent stray light from reaching the lens. Lens hood may also be helpful.

• Stop down to F5.6-8. Shut off ambient lights. Take photo. There shouldn't be any stray reflections because the only light reaching the lens is passing through the negative from behind.

As for whether to shoot the emulsion or base side, with ordinary film, I've tried both. When shooting the emulsion side, the image is sharper, but lighting isn't as even and color can be off because the base reflects light. When shooting through the base, imperfections in the base soften the image, but lighting is better because the emulsion scatters light.