- The whole system must be in a vacuum and therefore living specimens cannot be observed.
- A complex "staining" process is required and even then the image is in black and white.
- The specimen must be extremely thin.
- The image may contain artefacts. These are things that result from the way the specimen is prepared.
The image is a flat 2D image, but a 3D image can be built by looking at a series of photomicrographs produced. But this is a slow and complicated process.
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