Processing Of FFPE Tissue Samples

After the tissue samples have been collected, additional sorting, dissection, or microdissection may be required to isolate and prepare specific sections of tissue to undergo other processing steps. Today, fabric processing is often fully automated down to the final step, which can be combined manually.

Multi-step automation helps eliminate variation in the process as a source of variation in experimental results between different FFPE samples. However, if you also want to see the process of frozen tissue samples then visit

The Pros and Cons of FFPE vs Frozen Tissue Samples

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Fixation is the first step in treating tissue with FFPE. Important factors to consider include the solution used, the length of time for fixation, and the thickness and histological nature of the tissue sample to be fixed.


Another step in processing FFPE samples is dehydration. The reason for this is paraffin is unmixable with water, all the water in the formalin solution must be removed from the tissue before the paraffin can penetrate the tissue. A series of alcohol solutions are used to remove all water from the tissue.


Since the paraffin doesn’t actually mix with the alcohol, the next step is to remove the alcohol with a substance that mixes with the paraffin. This step is known as cleaning, and xylene is the most commonly used cleaning agent.

Paraffin Infiltration:

After adequate fixation, dehydration, and cleansing, the tissue may eventually undergo paraffin infiltration. Again, this step is not standardized and institutions around the world may use different mixtures of paraffin and wax with different compositions. Paraffin has different melting points and textures that affect the final block of tissue and its properties.