Agarose Embedding

Detailed help for making agarose and embedding cutting samples

What is Agarose Embedding?

“What is agarose embedding?” is one of the most commonly asked questions among customers interested in the Compresstome® vibratome. Agarose embedding is the process of embedding your tissue sample with agarose solution before you cut tissue slices with the Compresstome® vibratome. It can take some getting used to at first, yet 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. These agarose tablets make it easy for you to prepare agarose solution because they are pre-weighed, condensed tablets. After preparing your agarose solution, you will pipette the agarose over your tissue sample. Once the tissue is embedded, you will chill the agarose solution with a chilling block that is provided to create a Jell-O like consistency. 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.


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

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® vibratomes, some of them having used their model for 10+ years with great satisfaction. The Compresstome® vibratome was invented 14 years ago, and there has been a great deal of tests in-house and from scientists on both fresh and fixed tissue for agarose embedding. We have concretely concluded that agarose does not harm either fixed or fresh tissue at all during the embedding process.

Even after your slices are produced, the agarose rim will not harm your tissue. In fact, you can easily remove the agarose rim surrounding your tissue after it is cut. There are two methods for this: the first is to dip your tissue sample into a 30% sucrose solution before embedding, and this will allow the rim to fall off after it 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 thus it will fall off when your slice falls into the buffer tray and buffer solution.

Agarose Tablets

Here are detailed specifications and suggestions for making agarose solution with our agarose tablets!

Agarose Tablet Specifications

Gel Strength>1200 g/cm^2 (1%)
>2500 g/cm^2 (1.5%)
Gel Temperature36C (1.5%)
Melt Temperature88C (1.5%)
Moisture Content<10%
RNase/DNaseNone Detected
Protease/EndonucleaseNone Detected
StorageRoom Temperature
Buffer Tray Size110 x 60 x 30 mm

Making Agarose Solution

Buffer volume required to achieve agarose concentration:
Concentration1 Tablet2 Tablets