top of page

HREM Imaging Technique for 3D datasets

HREM also known as high resolution episcopic microscopy is a serial block face modified histology technique. Imaging samples from 1mm in field to 60mm and allowing for denser tissue.

HREM 3D stack mouse embryo
HREM 3D stack

What is HREM

HREM samples are embedded in resin and imaged by sectioning 1 micron - 10 microns with the remaining block face imaged. The staining technique used to prepare the samples is the key to imaging fantastic samples. The 2D images saved as TIFF/JPG/PNG/BMP can then be imported into most software packages and create 3D models for measurement.

Indigo HREM imaging system
Indigo HREM Imaging System

Imaging HREM samples

Imaging is performed using a specialised setup, consisting of a custom microtome, optics and software. Indigo scientific provides the complete package specifically designed for HREM imaging, but of course can be used for many serial block face imaging technology's such as EFIC.


Benefits of HREM

HREM offers many benefits over other technologies. Some of the most important are:

  • Imaging of denser tissue: with denser tissues and larger samples high-resolution episcopic microscopy excels.

  • No Clearing: HREM required no clearing of samples.

  • No interpolation or guess work: HREM produces a stack of images without using interpolation or guess work to achieve the resolution.

  • Flexible: HREM gives users great flexibility in use case from hearts to pups to plant matter HREM has been used in a variety of applications.

  • Resolution: HREM gives fantastic resolution for the geometry of samples, giving clear crisp images both in 2D and 3D analysis.

  • Cost: The optical HREM instrument will give fantastic 3D images for a fraction of the cost equivalent techniques. With low maintenance and an easily upgraded system HREM is easily integrated into most labs.



High Resolution Episcopic Microscopy has been used worldwide in the following applications:

  • Developmental embryo research. Whole embryos and individual organs.

  • Agricultural research (chicken embryos, plants etc)

  • Flys

  • Crocodile skin

  • Fish

  • Zebrafish

  • And more

Why not visit out Example page to see examples of images. You can also get in touch for a stack to visualise in your own 3D software.


Indigo Scientifics Optical HREM

Indigo Scientific has developed the Optical HREM alongside scientist using the instrument. The result is the latest revision as seen in our blog post, with faster acquisition, upgraded optics and more.

Indigo Scientific provides a complete serial block face imaging system, created solely for the purpose of serial block face imaging. With tailored optics and adaptability to enhance resolution, such as the setup for the XY acquisition module for scanning.

The benefits of Indigo scientific serial block face imaging system include:

  • Custom microtome for resin cutting, compatible with a range of blades. Indigo can provide adapters to fit any blade type on request. The microtome is designed by Indigo Scientific, specifically for the task of imaging, the setup is done in a way to not only leave a surface that is image ready but promotes safety. Indigos microtome does not leave the blade open to users and is not easy to interfere with outside of the experiment.

  • Tailored software here at Indigo we produce our own software for the job. As an independent company we can most likely fit in any request to be added into the software, wether it be a different light source, communication with a different device. We can help, the software already comes packed full of features to help with serial imaging, especially in HREM. Why not Contact Us to learn more.

  • Custom Hardware thanks to the design of the microtome it is easy to add additional hardware, such as an XY Scanning Stage. Although not essential this can significantly improve your resolution. As well as this Indigo also produce the stitches as you go along, we have tailored a stitching algorithm for imaging 3D datasets without those blocky lines. As well as this because HREM images are already aligned, no need for re-alignment. Our algorithm will produce perfect 3D data sets.

HREM Stitched mouse embryo
Stitched 6x6 Image using Indigo HREM
  • Flexibility not only for the technique but for the instrument. We are an enthusiastic imaging company ready for a challenge, we would like Optical High Resolution Episcopic Microscopy to be accessible to everyone and excel in research. By us being flexible to your needs in the machine, by adding new hardware software functions, we can help deliver new and exciting research.


Indigo offers an independent company mentality, with a friendly team and an ethos for open science we collaborate with our users to produce instruments for you. We like to offer fair pricing and products that will give you the best value for money, with long term support and upgradability in mind. Customer support is important to us, we will be here to ensure your product excels in your application. We like to ensure our customers receive the best we can offer with each sale so be sure to contact us to know more about the latest technology we offer.

Why not learn more here about what indigo scientifics deficatated HREM serial block face imaging instrument can do for your research. Or contact us for a demo or more information.


bottom of page