Cryosectioning vs Paraffin Embedding: Which One is Right for Your Research?

Not sure whether to choose cryosectioning or paraffin embedding for your tissue samples? This guide breaks down the pros, cons, and use cases for each method to help you decide.

Cryosectioning (left) vs Paraffin embedding (right)

Introduction

In the field of histology, the way you prepare your tissue samples can make or break your study. Two of the most common preparation methods—cryosectioning and paraffin embedding—offer distinct advantages depending on your research goals.

Whether you're studying tumour morphology, performing immunohistochemistry (IHC), or quantifying fibrosis in tissue sections, selecting the appropriate method for tissue sectioning and staining is essential for reproducible, high-quality results.

This blog compares these two essential histology techniques to help researchers, especially those in cancer research and tissue analysis, decide which method best suits their project.

What Is Paraffin Embedding?

Paraffin embedding is a standard technique in research histology for preparing high-resolution tissue sections. After fixation (commonly in formalin or 70% ethanol), the tissue undergoes dehydration, clearing, and infiltration with molten paraffin wax. Once embedded and cooled, the tissue can be sectioned using a microtome for H&E staining, special stains, or IHC.

Paraffin-embedded tissues offer exceptional morphological clarity, making this method ideal for studies requiring structural analysis.

Benefits of Paraffin Embedding:

Paraffin embedding is well-suited for:

• Long-term sample preservation and archiving

• Producing thin, high-quality sections for detailed tissue morphology

• Use with a wide range of histology stains, including routine H&E and special stains

• Compatibility with formal IHC protocols (with antigen retrieval)

Limitations:

• Tissue processing is time-consuming (typically overnight)

• Some antigenicity may be lost, requiring heat-induced epitope retrieval

• Not suitable for preserving lipids or enzyme activity

Paraffin embedding is best for research that demands detailed tissue structure, such as tumour grading, margin assessment, or fibrosis studies.

What Is Cryosectioning?

Cryosectioning is a faster tissue preparation method that involves freezing tissue samples, embedding them in a medium like OCT, and sectioning them using a cryostat. This method is preferred when sample preservation must prioritise protein function, lipid content, or enzyme activity over long-term structural integrity.

Frozen sections are useful in experiments requiring rapid tissue analysis or detection of fragile molecular targets that don’t survive routine processing.

Benefits of Cryosectioning:

Cryosectioning is ideal for:

• Rapid turnaround times—sections can be prepared in under an hour

• Preservation of native proteins, lipids, and enzyme activity

• Fluorescence-based immunostaining (immunofluorescence/IHC)

• Avoiding exposure to harsh solvents or heat

Limitations:

• Lower sectioning quality compared to paraffin (less crisp morphology)

• Greater risk of freezing artefacts if samples are not properly handled

• Frozen tissues require specialised cold storage

• Not optimal for long-term storage or routine structural analysis

Cryosectioning is best used in molecular biology and immunology-focused studies, where antigen preservation is critical.

Choosing the Right Histology Technique for Your Research

When deciding between cryosectioning vs paraffin embedding, consider the following key factors:

1. Research Objective

If you're analysing tissue architecture (e.g. tumour margins or fibrosis), paraffin is the superior choice. If you're detecting fragile proteins or doing enzyme histochemistry, opt for cryosectioning.

2. Speed and Workflow

Cryosectioning is significantly faster, making it suitable for time-sensitive projects. Paraffin embedding, though slower, offers robust, repeatable sectioning over time.

3. Staining Requirements

Most histology stains, including special stains like Sirius Red or Perls', work best on paraffin-embedded tissues. For fluorescent immunostaining, cryosectioned samples offer better antigen retention.

4. Storage and Archiving

Paraffin blocks can be stored at room temperature for years. Cryosections and OCT-embedded blocks require ultra-low temperature storage and are prone to degradation over time.

LabNexus Offers Expert Cryosectioning and Paraffin Histology Services

At LabNexus, we specialise in high-quality research-only histology services, offering both cryosectioning and paraffin-based tissue processing tailored to your needs. Our services include:

• Sectioning at requested thicknesses (4–10 μm)

• H&E, IHC, and a wide range of special stains

• Cryosectioning for fresh or fixed frozen tissues

• Digital slide scanning for image analysis

• Fast turnaround and affordable rates

We ensure all histology work is performed using modern, well-maintained equipment, and our team of trained professionals follow protocols designed for reproducibility and high fidelity.

Please note: LabNexus is a research-focused facility. We do not process or analyse samples for diagnostic purposes.

Need Help Deciding Which Histology Method Fits Your Study?

If you’re unsure which preparation technique suits your project, we’d be happy to assist.

Book a free consultation to speak with a LabNexus specialist. Whether you're exploring IHC, fibrosis models, or tumour analysis, we’ll help you select the most effective histology strategy.

References

1. Bancroft, J.D. & Gamble, M. (2020). Theory and Practice of Histological Techniques (8th ed.). Elsevier.

2. Kiernan, J.A. (2008). Histological and Histochemical Methods: Theory and Practice (4th ed.). Scion Publishing.

3. Culling, C.F.A., Allison, R.T., & Barr, W.T. (1985). Cell and Tissue Staining Techniques.

4. Ramos-Vara, J.A. (2005). Technical aspects of immunohistochemistry. Vet Pathol, 42(4), 405–426.