To some extent my preferences would be dependant on whether the images are to be shown as thumbnails or "full" size.
I'd rather scroll through a series of images than have what I think you are referring to as a carousel.
(I'm not a fan of those types of gallery where you see one large image and have to click on an arrow to see the next (or previous) image).
If the images are to be shown initially as thumbnails which have then to be clicked on to see the full size image, then it would seem logical to show any micro-structure images also as thumbnails, alongside the macro image thumbnail(s) for any given species.
If they are to be shown straight away at "full" size, then perhaps it might be better, (to avoid extensive scrolling), to show one "definitive" image for the species in question, and have a hyperlink to a separate page for any related macro/micro images.
For preference, my ideal would be a simple A-Z species list, with each included species also showing a representative thumbnail image, and hyperlinked to a separate "species specific" page for any additional images of that particular species. - Perhaps with some indication on the initial "species index" listing that micro-structure images are available.
Then it would be easy to search by species name, and it would be immediately obvious if additional /micro-structure images were available.
Or, if the species name wasn't known, the species thumbnail images could be browsed, to see if anything looked promising for the particular search.
If the species list is very extensive, then scrolling down an A-Z listing could become something of a chore - especially if searching for a Xylaria
species for example.
Perhaps separate tabbed pages for each letter might become appropriate, or maybe a set of "alphabet letters hyperlinks" near the top of the species index page such that any letter could be clicked on, taking the person searching directly to the first species name beginning with that letter?