As you read descriptions of various histological features in this website, remember that microscope slides are made by taking a thin section of specimen, staining it and placing the section on a slide beneath a cover slip.  Stains are used to highlight various structures that respond differentially to the various chemicals used.  For example, nuclei often appear blue or dark purple while the cytoplasm stains pink or orange.

Also keep in mind that you are looking at three dimensional objects in two dimensions.  Thus, viewing a series of tall (columnar) cells from the top will fail to reveal their true  shape.   In addition,  a section from the same tubular organ can appear very different depending on the precise plane of the cut when the tissue was sectioned.   Furthermore, what you can or cannot see may also depend on where the cut  was made when the tissue was sectioned.  For example, if you are looking down on a tall cell sectioned near the top, a nucleus found near the bottom of the cell will not be present.  Often the exact boundaries between cells cannot be discerned.  Although  these problems can sometimes be frustrating, your confusion can be minimized by viewing more than one slide and understanding the nature of these limitations.