Before microscopes were first used in the seventeenth century, no one knew that living organisms were composed of cells. The first microscopes were light microscopes, which work by passing visible light through a specimen. Glass lenses in the microscope bend the light to magnify the image of the specimen and project the image into the viewer's eye or onto photographic film. Light microscopes can magnify objects up to 1,000 times without causing blurriness.

Magnification, the increase in the apparent size of an object, is one important factor in microscopy. Also important is resolving power, a measure of the clarity of an image. Resolving power is the ability of an optical instrument to show two objects as separate. For example, what looks to the unaided eye like a single star in the sky may be resolved as two stars with the help of a telescope. Any optical device is limited by its resolving power. The light microscope cannot resolve detail finer than 0.2 micrometers, about the size of the smallest bacterium; consequently, no matter how many times its image of such a bacterium is magnified, the light microscope cannot show the details of the cell's internal structure.

From the year 1665, when English microscopist Robert Hooke discovered cells, until the middle of the twentieth century, biologists had only light microscopes for viewing cells. But they discovered a great deal, including the cells composing animal and plant tissues, microscopic organisms, and some of the structures within cells. By the mid-1800s, these discoveries led to the cell theory, which states that all living things are composed of cells and that all cells come from other cells.

Our knowledge of cell structure took a giant leap forward as biologists began using the electron microscope in the 1950s. Instead of light, the electron microscope uses a beam of electrons and has a much higher resolving power than the light microscope. In fact, the most powerful modern electron microscopes can distinguish objects as small as 0.2 nanometers, a thousandfold improvement over the light microscope. The period at the end of this sentence is about a million times bigger than an object 0.2 nanometers in diameter, which is the size of a large atom. Only under special conditions can electron microscopes detect individual atoms. However, cells, cellular organelles, and even molecules like DNA and protein are much larger than single atoms.

Biologists use the scanning electron microscope to study the detailed architecture of cell surfaces. It uses an electron beam to scan the surface of a cell or group of cells that have been coated with metal. The metal stops the beam from going through the cells. When the metal is hit by the beam, it emits electrons. The electrons are focused to form an image of the outside of the cells. The scanning electron microscope produces images that look three-dimensional.

The transmission electron microscope, on the other hands, is used to study the details of internal cell structure. Specimens are cut into extremely thin sections, and the transmission electron microscope aims an electron beam through a section, just as a light microscope aims a beam of light through a specimen. However, instead of lenses made of glass, the transmission electron microscope uses electromagnets as lenses, as do all electron microscopes. The electromagnets bend the electron beam to magnify and focus an image onto a viewing screen or photographic film.

Electron microscopes have truly revolutionized the study of cells and cell organelles. Nonetheless, they have not replaced the light microscope. One problem with electron microscopes is that they cannot be used to study living specimens because the specimen must be held in a vacuum chamber; that is, all the air and liquid must be removed. For a biologist studying a living process, such as the whirling movement of a bacterium, a light microscope equipped with a video camera might be better than either a scanning electron microscope or a transmission electron microscope. Thus, the light microscope remains a useful tool, especially for studying living cells. The size of a cell often determines the type of microscope a biologist uses to study it.

在17世纪显微镜第一次投入使用之前，人们都不知道生物体是由细胞构成的。第一代显微镜是光学显微镜，其工作原理是将可视光透过样本。显微镜中的玻璃镜片通过弯曲光线将样本放大，并将样本的影像投进观察者的眼中或者感光胶片上。

光学显微镜能将物体放大1000倍而不会模糊不清。将物体的视尺寸放大是显微镜学的一个重要因素。另一个重要因素是分辨率，即影像的清晰度。分辨率使得光学仪器将两个物体区分开来。例如，天空中的星星，在肉眼看来是一颗，但借助望远镜观察之后会发现其实是两颗。任何光学仪器都受到分辨率的制约。光学显微镜不能够分辨小于0.2微米的细节，这相当于最小的细菌的大小；因此，不论这个细菌被放大了多少倍，光学显微镜都不能展现出细胞内部结构的细节。

从1665年英国显微镜学家Robert Hooke发现细胞到二十世纪中期，生物学家只能通过光学显微镜来观察细胞。但是他们也发现了许多东西，包括组成动植物组织的细胞、微观生物体以及细胞内的一些结构。直到19世纪中期，这些发现促成了细胞学说，指明所有的生命体都是由细胞构成的，而细胞又都是由另外一些细胞构成。

直到二十世纪50年代，由于电子显微镜的使用，我们对于细胞结构的了解实现了巨大飞跃。不再利用光线，电子显微镜利用的是电子束而且比光学显微镜具有更高的分辨率。实际上，现代最先进的电子显微镜能够识别直径为0.2纳米的物体，比光学显微镜进步了成千倍。在本句话末尾的那个句号在直径上比一个大一点的原子0.2纳米的直径大了一百万倍。只有在特殊情况下电子显微镜才能发现原子。但是，细胞、细胞器、甚至像DNA和蛋白质这样的分子都比单个的原子要大得多。

生物学家使用扫描电子显微镜研究细胞表面的具体构造。细胞或者细胞群被覆盖上金属涂层。电子束扫描细胞的时候，金属涂层阻挡住电子束进入细胞内。当电子束击中金属的时候，金属将电子发射出去。因此，电子的聚集显示出了细胞的轮廓。扫描电子显微镜的成像看起来是三维立体的。
另一方面，透射电子显微镜被用来研究细胞的内部结构。样本被切割成极其薄的切片，透射电子显微镜将电子束穿透切片，正如光学显微镜将光束透过样本一样。但是，与光学显微镜不同的是，它不是用玻璃作为镜片，而是使用电磁体作为镜片，正如所有的电子显微镜一样。电磁体弯曲了电子束去放大影像，并将影像投在观察屏上或感光胶片上。

电子显微镜的确彻底变革了对细胞和细胞器的研究。但是，它并没有取代光学显微镜的地位。电子显微镜的局限性之一是，它没法用来研究活的样本，因为样本必须保存在真空的空间里；也就是说，所有的空气和液体都必须被去除。如果一个生物学家正在研究一个活体过程，比如一个细菌的旋动，装备有摄像机的光学显微镜就比扫描电子显微镜或透射电子显微镜好用了。因此，光学显微镜仍是一个有用的工具，尤其是研究活的细胞的时候。细胞的大小经常决定了生物学家选用哪种显微镜来研究它。