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Modeling small 3D stuff in 2D photos requires similar strategies to large objects.
The key light (off-axis frontal source) creates highlight clues on the higher parts of the front of the object the camera sees. Fill is the frontal source added because the sensor can't handle the contrast created by the key light. Part of what makes artificial lighting look natural (normal) or not is whether the highlight and shadow clues wind up in the same places and shadows at similar downward angles. That's why this looks odd:
When flash shots look obvious and "fake" its because the angle of the key light is unnaturally low. So direction of the flash is important to how the content is perceived as being natural or not, even in macro subjects:
Those above are all dual flash shot compare the modeling in those with this one with a single flash above the camera:
Natural light can come from both those directions, but side / back lighting is needed to create the illusion of 3D in the 2D photo via the contrast between the highlights the key light creates over the foundation of fill that lifts the shadows.
The natural model for key and fill are sun and sky light. I did this exercise to illustrate how mid-afternoon natural light creates easily recognized patterns on a face when the key light is placed 45° above the eyes and 45° to the side of the sundial shaped nose:
One conventional strategy for lighting faces is to put the key light in front at about 45° above the eye line to get it in the eyes and 45° to the side, because that models the 3D shape of the nose nicely. That's the pattern seen in the snow head shot above. Here's the same lighting from different positions around the face.
The take away lesson there is that step one is orienting the subject to the key light.
In the case of the snow head I knew exactly where the sun would be in the afternoon from previous observation.
In natural light you need to position a subject to the light. In the shots above the light in all of them is 45°V45°H from the center of the nose. What changed was the camera position 0°, 45°, 90°, and 135° from the sun for the broad oblique, full face, short oblique and profile views respectively.
When the key light gets back greater than 90° from the camera its usually called "rim" light rather than "key" to avoid confusion when both are used together. Don't get hung up on the names, understand how the direction of the dominant source creating the brightest highlights affects modeling.
This is a shot taken at the National Arboretum in Washington with a flash on my bracket w. diffuser for frontal / downward fill and the key lighting coming from a flash with diffuser held out in my arm above and behind the plants.
This shot was done as a demo for a maternity lighting strategy to reveal the shape of stomach without it looking like a blimp. I used an egg as a stand in since I didn't have a pregnant woman available:
I use that shot to illustrate that for most non-human subjects the modeling looks more 3D in a 2D photo when the brightest highlights are created from a source behind the subject at 135° to the lens axis.
None that is typical "macro" lighting, but then most conventional macro lighting doesn't model naturally.
Macro ring lights create flat shadowless light. They were first developed for medical documentation where shadowless light was needed in photographs of mouths and surgical incisions.
But macro ring lights are ideal for fill light with macro lenses because they solve the problem of getting the fill flat and even when the subject is only an inch or so from the front of the lens. Put the fill anywhere else and the lens will shade it. That's not a problem with longer macro lenses like the 100mm because there's a bigger gap between lens and subject.
You may have seen the MR-24 dual macro flash on opposite sides level with the lens. Putting lights level at opposite 45° angles is a great strategy for copying a book but will not create natural looking 3D modeling. What is does do very effectively is put large symmetrical catchlights on the bulging eyes of bugs in macro shots which make them very strong focal points.
With bugs and small critters its relatively easy to get the light behind the subject. Wimberley and others make macro brackets with long arms to do that.
I don't shoot macro very often and already have a pair of 580ex flashes so I created this DIY macro diffuser out of some mat board. It bounces the light back towards the camera then forward again directly above and to the sides of the lens:
Used by itself it put the highlight and shadow clues in the "right" places to make objects look natural:
Using it in tandem with an off camera slave from behind as "rim" lighting enhances the 3D modeling:
Since the diffuser on the camera moves with the camera and the distance and angle of the rim lighting from the flash behind isn't critical its logistically simple. Since I already had the flashes the only cost was the cardboard which I had already from matting photos.
Outdoors I usually use the sun as rim light and light the front side with a single flash on my bracket..
The same strategy can be used with flower shots...
that one was taken with flash on the bracket but in a close-up macro you'd get similar modeling with the DIY diffuser: not flat fill, lighting more similar to skylight which is brighter from above than the sides.
It doesn't require a lot of gear or complicated logistics, just an understanding of how light creates the illusion of 3D in 2D photos. That's pretty simple also. Things look most naturally 3D in 2D photos when the light is above the object and the camera shoots into the shadows of the "key" or "rim" lighting. Fill needs to reach the areas that light doesn't hit from the direction of the lens.