Red is a very difficult colour in red/cyan anaglyphs.
As explained on the anaglyph page, red is seen only in the right eye as it leaks through the cyan filter. The left, red filtered eye, only sees monochrome.
More red leaks through cyan filters if the red channel in the anaglyph is made brighter and the blue and green channels darker, but at the cost of retinal rivalry. The left eye now sees a brighter picture than the right. By using an extra dark red filter, the retinal rivalry is reduced.
Anachrome and Mirachrome glasses have this dark red filter and will give a better result. However, the better result is only for red intensified anaglyphs, like this one. Proview red/cyan acrylic lenses will show red fairly well in this case, where red has been given a pretty hard boost! (The background was blue, but with the red boost it is not any more.) Cardboard mounted gel filters may only show brown rather than red. IYF goggles are excellent for cutting ghosts, but will fail to show red in this anaglyph.
Close your right eye to see how the left, red filter is not giving any colour information. Colour all depends on the right eye. The left eye is for stereo parallax.
Now have a look here, for the same flower (at lower magnification), to see that ColorCode filters show red better - and can also show blue at the same time.
The depth of field in macro photography is limited. Closing the lens aperture improves depth of field, but at the expense of a reduction in resolution due to diffraction. In this case, the aperture was kept fairly wide (f8) where I know diffraction is not a problem with my lens. Multiple pictures were taken by winding the camera closer and closer to the flower, until the far side was in clear focus. The multiple images were then stacked in Helicon Focus program. The whole process had to be repeated after moving the camera sideways to make the stereo pair. Naturally the flower had to be in water so it would not wilt while all this was going on!
How to make and view anaglyphs
Stereo Home Page