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Tissue Processing For Histology: What Exactly Happens?

Posted in: Microscopy and Imaging
Image of toilet tissue as a pun about tissue processing for histology

When preparing a sample (or multiple samples) for histology, there are multiple steps required. We’ve covered these steps in brief in a previous article on How Histology Slides are Prepared, but this article will focus on one particular procedure that needs to take place between tissue fixation and the embedding/sectioning of paraffin blocks: tissue processing for histology.

You simply can’t take fixed tissue and embed it! We have already introduced tissue fixation and tissue embedding/sectioning previously, so please read those articles for more information on the other steps involved in tissue preparation.

In this current article, we focus on this in-between stage of conventional tissue processing for histology.

6 Steps of Histology Tissue Processing

1. Get Your Pencil Out

Following fixation, the tissue sample is transferred to a tissue cassette. These come in various sizes and hold and protect the tissue while it undergoes processing.

Once the embedding stage is reached, the cassette lid is snapped off, and the main part of the cassette forms a base for the paraffin wax block. The cassettes can be labeled by hand (with a pencil!) or your histology lab may have a cassette labeling machine.

There are three main steps in tissue processing, namely: ‘dehydration’, ‘clearing’, and ‘infiltration’. Each of the steps of the processing method involves the diffusion of a solution into tissue and dispersion of the previous solution in the series.

2. All the Fun of the Carousel

In most modern institutes and labs, tissue processing for histology will be carried out in dedicated tissue processing machines. The older design of machine is a carousel, which contains a cage where the tissue cassettes are placed.

This carousel has a number of glass beakers containing solvents and solutions that ensure the tissue is dehydrated and cleared, ready for paraffin wax embedding. The carousel vertically agitates the cage in each solution before moving on to the next solution in the dehydration/clearing method.

The modern processors have a chamber in which the specimens are held, and the different solutions are pumped in and out of the chamber. In general, the whole process takes around six hours and is usually set up to run overnight.

3. First, Remove the Water

First, the tissue needs to be dehydrated to remove the water, which is present either free or bound to the tissue. Paraffin wax is hydrophobic; therefore, most of the water in the tissue must be removed before it can be infiltrated with wax.

Removing the water is carried out by immersing tissue in a series of ethanol solutions of increasing concentrations until 100%, water-free alcohol is reached. A series of increasing concentrations is used to ensure that the water in the tissue is gradually replaced by the alcohol and to avoid excessive distortion of the tissue.

Various components of the cell are also removed by this process. At the lower end of the ethanol concentrations, water-soluble proteins are removed, while towards the 100% ethanol step, certain lipids may be dissolved.

4. Ethanol and Wax Don’t Mix

Although the tissue reaches the final stage of dehydration in 100% ethanol, it’s not possible to proceed straight to wax embedding, as ethanol and wax don’t mix!

This is where tissue clearing comes in. The term clearing refers to the property of the solvents used—they have a relatively high refractive index, and when tissue is immersed in it, it becomes transparent and clear.

5. It’s Becoming Clearer…

The solvent used for this intermediate stage is usually xylene. The ‘clearing agent’ needs to be miscible with both ethanol and paraffin wax.

Following dehydration, the tissue is immersed in one to three different xylene immersions. In these stages, the ethanol is gradually replaced with xylene, and when the tissue is embedded, the xylene will be replaced by the molten paraffin wax.

Shrinkage of tissue can occur at these final stages as the xylene also removes fat residues left in the samples.

6. At Last – A Block!

The final stages are called ‘infiltration’ and ‘blocking out’. Infiltration is when the final xylene is replaced with molten wax, which infiltrates the tissue. Again, this is typically three different wax immersions to ensure that none of the clearing agent remains in the tissue.

After the final infiltration, the tissue cassettes are transferred to an embedding station. This machine has reservoirs of molten wax, hotplates, and a cold plate for setting the tissue blocks.

The infiltrated tissue is removed from the cassette and orientated within a suitably sized metal mold. The mold is filled with molten wax, the main part of the labeled cassette is placed on top, and this is also filled with wax. The whole mold is transferred to the cold plate to finally set.

That ends the journey from tissue to wax block, which is, I guess, the start of another journey of sectioning, making slides, and immunohistochemistry!

Finally, below is a table that highlights the typical main stages of tissue processing for histology.

Table 1. Main stages of tissue processing for histology.

Dehydration70% alcohol60 mins
Dehydration90% alcohol45 mins
DehydrationAbsolute alcohol45 mins
DehydrationAbsolute alcohol45 mins
DehydrationAbsolute alcohol60 mins
ClearingXylene60 mins
ClearingXylene60 mins
ClearingXylene60 mins
InfiltrationParaffin wax30 mins
InfiltrationParaffin wax60 mins
InfiltrationParaffin wax90 mins
Blocking OutParaffin waxn/a

Do you have any questions about tissue processing for histology microscopy? Leave a comment below!

Want to know more about histology? Visit the Bitesize Bio Histology Hub for tips and tricks for all your histology experiments. You might also be interested in the later steps of sample prep for histology, which are covered in our eBook guide to special stains in histology, and immunohistochemical staining article.

And if you’re wondering what histological stain will stain the tissue you’re interested in? Download our free, colorful guide to histological stains and pin it up.

Originally published December 10, 2013. Reviewed and updated October 2021.

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  1. Jacky Lam on October 2, 2019 at 11:13 pm

    So helpful, thanks a lot

  2. nsikan ebong on August 3, 2019 at 10:36 pm


  3. AbKadir RIfaei Rashid Khairi on June 17, 2019 at 6:11 am

    Thanks. Can a fatty tissue completely dissolves and dissappears after tissue processing?

  4. Frans on June 7, 2019 at 3:16 pm

    How long does it take to infiltrate wax in fish ovaries? I did it using the procedure described on this article, it didn’t work and then left it in the oven overnight but still it just doesn’t work. Everytime I section there are holes on my sections where the tissues is supposed to be.

  5. changtoek on February 25, 2019 at 7:18 am


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