Im glad you brought up the challenges of extrapolating from a 2-dimensional view to what the actual 3-dimensional object is like.

For the particular case of amoebas, they dont have a set shape. Their shape constantly changes as they extend pseudopodia, retract them, send out pseudopodia of different sizes and from different locations, and such. They dont float freely very often because pseudopodia really only work for locomotion on a surface. When they engulf something, you can still see it because the amoebas are mostly clear, so even when its completely inside, its still visible.

Theres a great site for thinking about how 3-dimensional objects look in cross section:

I like to use this as an exercise in observation (what you can see directly) and inference (the conclusions you draw from observations). For example, if a student says something is sticky or crunchy, I ask them what observations make them think that (make that inference).

There are great geometry and art questions in this. For example, they notice that a cylinder and a cube look the same in cross section. They can talk about strata or layers. You can discuss how a section at a different angle would produce a very different image.

Theres good language arts skill-building in getting them to write clear descriptions.

Just a warning, in the UK, they have a product called Smarties that is very similar to our m&ms. This is a good opportunity to bring up why we use scientific names that are understood all over the world.

The amoeba is 3-dimensional, with pseudopods reaching out in different directions.I think you might be seeing a slide at an early stage, where the pseudopods have reached around the bacterium, in 3 dimensions, but the food vacuole hasn't separated from the plasma membrane of the amoeba yet. I think the bacterium in the food vacuole will look like a separate object inside the amoeba for a while, before it gets digested. The amoeba is sort of transparent, so you are probably looking through some of the cytoplasm.

I don't think I've seen live amoeba either. I looked at water with algae in it recently, and I saw Paramecium. These paramecia looked thin and hungry to me. But maybe I should only say they looked thin, because 'hungry' might be too complex a feeling for a paramecium. It is amazing how much these single-celled protozoa can do and sense. My grad student research was about 'behavior' in Paramecium. There were mutants that had different behavior. For example, one mutant could only swim forward, so it just swam in circles around the edge of the depression slide, because it didn't back up when it bumped into the edge. Those mutants were called 'pawns,' like the chess pieces that can only move forward. Ching Kung found this mutant. He is at the University of Wisconsin.

When food is engulfed by an amoeba it is taken inside the body of the amoeba and stored in a food vacuole. The bacteria is then surrounded by the amoeba but since the amoeba is transparent and thin, it is difficult to tell. The pseudopods are only considered pseudopods temporarily as they reach out and engulf the bacteria. Once they have retracted back to the amoeba they are no longer considered pseudopods, but become a regular part of the amoeba until they extend again to look kind of like arms. Amoebas can have different shapes and sizes depending on the species and change shape slightly as they move by extending their pseudopods.

Amoebas are, indeed, three-dimensional organisms, and it is possible to see right through them, thus seeing the bacteria inside of their vacuoles. The cover slips do flatten out the water that the amoebas are living in, but there is still space for them to inhabit in-between the slide and cover slip. In open water, amoebas can take, quite literally, whatever shapes they want.