Safety of Agarose Embedding for Tissue Slicing

Agarose embedding illustration

What is Agarose Embedding?

“What is agarose embedding?” and “Do I need to embed my tissue in agarose?” are some of the most commonly asked questions among customers interested in the Compresstome® vibrating microtome models. Agarose embedding is the process of embedding your tissue sample with low-melting agarose solution within our Compresstome® Specimen Tubes. This step is done before you begin cutting tissue slices with our Compresstome® models. While this is a unique protocol to using the Compresstome® slicers and may take some getting used to, with practice, this process ultimately takes only a fraction of the user’s time for sectioning overall and aids in the production of healthier and smoother tissue slices.

Why Use Agarose?

The agarose tablets we provide (found here) are low-melting point agarose. We include these agarose tablets in all Compresstome® orders that contain our Starter Kits, as well as selling them individually. Our agarose tablets make it easy for the user to prepare agarose solution for embedding, saving you time because they are pre-weighed, condensed tablets. After preparing your agarose solution, the user will pipette the agarose over their tissue sample within the specimen tube. Once the tissue is embedded, the user will chill the agarose solution with an already cold chilling block (that is provided with all Compresstome® orders) to create a Jell-O like consistency of agarose surrounding your tissue sample. The agarose gel gives the tissue sample 360° stability inside the specimen tube, so your tissue sample will never fall off or shift positions throughout sectioning.

Agarose embedding process

The agarose gel also aids in the unique compression technology that our Compresstome® vibrating microtomes are known for. Agarose gel keeps the tissue stable during sectioning and assists with the slight compression on your tissue sample as it is being cut to create even, smooth, consistent slices that are filled with healthy cells every time you produce a slice with the Compresstome®.

Agarose embedding gentle compression benefits

Will Agarose Harm My Tissue?

Using agarose will not harm your tissue. In fact, there are hundreds of users around the world who own and use Compresstome® vibrating microtome models, some of them having used their model for 10+ years with great satisfaction. The Compresstome® slicers were invented 16 years ago to produce healthier slices for patch-clamp electrophysiology experiments. Since that time, there has been a great deal of tests in-house and from scientists for agarose embedding on both fresh and fixed tissue. We have concretely concluded that agarose does not harm either fixed or fresh tissue at all during the embedding process. Through invention, testing, and finally, conclusion, we are confident that our agarose embedding method ensures the safety of the tissue samples and health of the produced slices for many different experiments.

After your slices are produced, the agarose rim will still not harm your tissue. In fact, you can easily remove the agarose rim surrounding your tissue after it is cut if needed. There are two methods for this: the first is to dip your tissue sample into a 30% sucrose solution before embedding, and this will act as a gentle “film” between your sample and the agar rim, aiding the agar rim to fall off after the slice is cut. The second method is to use a higher concentration of agarose when preparing your solution. This will result in a firmer agarose gel and will fall off the produced slices when your slice falls into the buffer solution of the Compresstome® buffer tray.

Embedding your tissue in agarose within the specimen tube is essential for receiving the compression advantage our Compresstome® vibrating microtomes provide on your produced slices. We want our customers to succeed using our Compresstome® models, and this includes the agarose embedding step in order to produce the best slices in conjunction with our patented compression technology.

Related Posts
Compresstome Vibrating Microtomes

Customer Testimonials at Precisionary Instruments

At Precisionary Instruments, we have almost two decades of customer service experience and microtome expertise. We have strategically built our brand to be trusted in


How sex hormones sculpt the brain

Sex hormones are hormones that play a role in the development and maintenance of the male and female reproductive systems, as well as secondary sexual

Compresstome Vibrating Microtomes

Introduction to Patch-Clamp Electrophysiology

Electrophysiology is the study of the electrical properties of biological cells and tissues, and how these properties generate and propagate electrical signals in the body.

Call Now Button617-682-0586