Microtomy Master: Tips and Tricks to Tackle Stubborn Tissue Blocks

By Mike Nelson, Lab Operations Manager, and Elsa Bowers, Histology Technologist, Reference Medicine

As virtually all lab techs know, the practice of microtomy requires a delicate balance between speed and precision, and between tissue preservation and usability – balancing acts with high stakes (with a lot hanging in the balance, you might say). Every tissue section you produce is a step toward answers for patients and their families -- and your job is to provide the best possible sample to pathology to support the diagnostic journey that leads to treatment. 

Whether preparing tissue sections for microscopic examination, immunohistochemistry (IHC), or next-generation sequencing (NGS), lab technicians face the ongoing challenge of producing high-quality sections with a variety of provided specimens. 

While some blocks cut effortlessly, others -- like dry liver or fatty breast tissue -- can be daunting. Some tissues resist clean sectioning due to their natural properties, while others require extra hydration​​. 

Your goal as a lab technician is to adapt to these challenges and deliver the best possible sections for pathologists to examine.

And while you can’t always control the specimen you receive, you can control how you process it.

Here are a few of our top tips and tricks to make the most out of the specimen you have and avoid common microtomy missteps.

1. Start smart.

• Ensure you have a stable block by cleaning off any paraffin residue from the cassette edges and avoid overfilling during embedding. This helps the block sit firmly in the holder to enable more even cutting. 
• To prevent uneven sections, tighten the knife and block holders securely, but avoid over-tightening—too much pressure can damage the microtome. 
• Verify your micron settings before cutting. A quick check ensures the section’s thickness matches your lab’s requirements​.
• Always wear gloves when handling slides to prevent transferring skin cells or other contaminants​ to your section.

An unstable, unsecured block (left) versus a stable, secured block (right).

2. Keep your cool (or warm) and hydrate.

• Rehydrate dry tissues like liver by soaking the block in a water bath for about 15 seconds. Chill briefly on ice before sectioning​.
• Fatty samples like breast tissue can expand or “explode” in the water bath. Reduce the water bath temperature for fatty tissue to prevent this disaster and keep your sections intact​​.
• Extend soaking time for tissues with calcium deposits to ease cutting; but monitor closely—results can vary​.
• Air bubbles lurking at the bottom of the water bath can rise up and distort sections. Use your forceps to clear bubbles before placing ribbons in the bath​.

A block rehydrating in a water bath.

3. Control yourself.

• Cool your forceps in an ice bath before handling sections to mitigate unwanted sticking​.
• Transfer ribbons smoothly by lifting the ends into a U-shape for better control as you move them to the water bath​.
• Blocks that are too cold can resist sectioning or fail to form ribbons. Try gently pressing the block with your hand to warm it up for smoother cutting​.

Forceps being cooled in an ice bath before handling sections.

4. Make the cut.

• Dense tissue like uterus require a steady, rhythmic cutting motion. Moving too slowly or erratically can create sections that are too thick or thin​.
• Always lock the cutting wheel when you’re not actively sectioning to prevent injury and accidental movement that could damage the block​.
• When facing a block, check for shiny areas – leftover paraffin -- that indicate incomplete tissue exposure. Stop when you’ve exposed enough tissue to avoid unnecessary waste​.

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‍It’s in your hands.

Not every block comes to you perfectly processed. Sometimes you’ll receive under-processed samples or external lab blocks that aren’t ideal. Recognize that you can’t control how the tissue arrived -- only how you respond – and be patient and thoughtful. 

Also, recognize that each lab is different. At Reference Medicine, we are focused on quality and precision, but some labs prioritize speed and quantity. If your lab is quantity-driven, finding small efficiencies can help you achieve better results without slowing down.

‍Manage the Unmanageable

Microtomy is both a science and an art. Each tissue block presents a unique challenge, and your experience informs how you react to each specimen to produce clean, clear sections for pathology so they can deliver accurate diagnoses. Every section you produce transforms tiny tissue samples into critical answers, guiding patients and their families toward hope, healing, and the next steps in their journey.