Laboratories working with tissue sectioning often compare microtomes and cryostats when selecting the right equipment for their workflow. While both systems are designed to produce thin tissue sections for analysis, they operate differently and are suited to different applications within histology, pathology and research environments.
Understanding how each system works, the types of samples they are designed for, and how they fit into laboratory workflows can help improve section quality, reduce processing issues and support more efficient diagnostics or research outcomes.
If you need guidance choosing the right sectioning system for your laboratory, our team can help based on your application and workflow requirements.
A microtome is a precision instrument used to cut extremely thin sections of embedded tissue for microscopic analysis. In most histology laboratories, microtomes are commonly used with paraffin-embedded tissue samples to produce consistent sections for routine staining and examination.
Rotary microtomes are among the most widely used systems in histopathology due to their accuracy, repeatability and ability to produce thin sections suitable for high-resolution analysis.
Microtomes are commonly associated with routine histology workflows where section consistency and long-term specimen handling are important. In our experience, laboratories processing high sample volumes often prioritise reliability and repeatability over sectioning speed alone.
The Bright Instruments Rotary Microtome 7010 is designed to deliver precise, repeatable tissue sectioning for routine paraffin-based laboratory workflows.
The Rotary Microtomes 7010/A and 7010 from Bright Instruments are expertly designed and built to deliver exceptional performance.
A cryostat is a refrigerated sectioning system designed to cut frozen tissue samples at low temperatures. The instrument combines a freezing chamber with a microtome-style cutting mechanism, allowing tissue to remain frozen during sectioning.
Cryostats are commonly used in applications where rapid section preparation or preservation of biological structures is important, particularly during intraoperative procedures and certain immunohistochemistry workflows.
Because tissue is sectioned while frozen, cryostats can help preserve biological properties that may be altered during paraffin processing.
For laboratories working with frozen tissue workflows, the Bright OTF7000 Cryostat is designed to support stable temperature control, usability and day-to-day sectioning consistency.
Although both systems are used for tissue sectioning, they are designed for different laboratory requirements and sample preparation methods.
One of the biggest differences between the two systems is the method of tissue preparation. Microtomes rely on processed and embedded tissue blocks, while cryostats work directly with frozen specimens.
Selecting between a microtome and cryostat is rarely about which system is “better”. The right choice depends on the type of samples being processed, turnaround expectations and the overall laboratory workflow.
For example, laboratories performing routine histology and high-volume paraffin sectioning often prioritise consistency, throughput and long-term sample storage. In these environments, microtomes are typically the preferred solution.
Cryostats, on the other hand, are often chosen when rapid tissue analysis is required. Frozen sectioning can support quicker diagnostic decisions during surgical procedures and may help preserve biological structures that are sensitive to standard processing methods.
We’ve found that workflow requirements are usually a more important consideration than speed alone when selecting sectioning equipment.
Microtomes are widely used in routine histopathology and paraffin-based workflows where precise, repeatable tissue sectioning is required. They are particularly well suited to laboratories handling high sample volumes or requiring long-term specimen archiving.
Common applications include:
Rotary microtomes are often selected for environments where consistency and fine structural detail are priorities.
Cryostats are commonly used in workflows where frozen tissue sectioning and rapid turnaround are required. This includes intraoperative pathology, immunohistochemistry and research involving temperature-sensitive specimens.
Because frozen sections can be prepared quickly, cryostats are often used when immediate tissue analysis is needed during surgical procedures or specialist research applications.
Learn more about how to optimise cryostat temperature for frozen tissue sectioning to help improve section consistency and reduce common cryosectioning issues.
Temperature-related cryosectioning artefacts and how to fix them
In many laboratories, both microtomes and cryostats are used together as part of a broader tissue sectioning workflow.
A microtome may be used for routine paraffin sectioning and archived specimen analysis, while a cryostat supports frozen section diagnostics and rapid tissue assessment.
Using both systems allows laboratories to adapt to different sample types, diagnostic requirements and research applications without compromising section quality or workflow efficiency.
Selecting the wrong sectioning system can lead to workflow inefficiencies, inconsistent section quality and unnecessary processing challenges.
A common mistake is choosing equipment based on speed alone without considering sample preparation methods, laboratory throughput or maintenance requirements. In some cases, frozen sectioning may be selected when paraffin processing would provide more consistent long-term results.
In our experience, understanding the intended application and sample type early in the selection process helps avoid many of these issues.
6 Common Sectioning Mistakes (and How to Fix Them!)
What is the difference between a cryostat and microtome?
A microtome is typically used to section paraffin-embedded tissue at room temperature, while a cryostat sections frozen tissue within a refrigerated chamber.
Are cryostats used in histology laboratories?
Yes. Cryostats are commonly used in histology and pathology laboratories for frozen sectioning and rapid diagnostic procedures.
Can a cryostat replace a microtome?
Not entirely. Many laboratories use both systems because they support different workflows and tissue preparation methods.
Why are cryostats kept at low temperatures?
Low temperatures help preserve tissue structure and biological properties during frozen sectioning.
What tissues are commonly processed using a microtome?
Microtomes are commonly used for paraffin-embedded tissue samples in routine histology and pathology workflows.
Choosing the right tissue sectioning equipment depends on your laboratory workflow, sample type and diagnostic requirements.
Whether you are looking for a rotary microtome, cryostat or guidance on selecting the right system for your application, our team can help.
We also provide ongoing laboratory equipment servicing and support packages to help laboratories maintain long-term sectioning performance and minimise downtime.
Contact us for any enquiries. Whether you’re looking for a new cryostat, microtome or rapid freeze unit, need spares or servicing, or are interested in becoming a Bright distributor, our team is here to support you.
