top of page
Mouse Heart 3D Cut Through

Optical HREM Applications

Optical High-Resolution Episcopic Microscopy Use Cases and Benefits for 3D Imaging

Partially sectioned catfish embryo imaged with HREM, revealing internal structures including gills, heart, and developing organ systems.

Why HREM?

Imaging dense biological and agricultural samples has often proven difficult as they are hard to clear/image. We provide a solution to this by combining sectioning with imaging, HREM provides close to histology images with a 3D perspective for quantitative analysis or visualisation, the instrument has been used in a variety of applications but is still expanding.

Throughout the years our instruments have grown to provide extra capabilities such as scanning and improved imaging. This results in even greater possibilities in sample possibilities.

Here we look at a few of the applications HREM has been used in and why it takes advantage.

What is HREM Used For?

Developmental Biology & Embryology

HREM offers a unique approach to imaging embryos of varied species from the easier Zebrafish to the denser Mouse and Chick embryos. It offers this with no distortion, missing sections or clearing required.

  • Optical HREM systems offer high resolution on larger volumes, down to 1 micron in the axial direction. Ideal for visualising blood vessels and similar features

  • Quantify organ volumes of mice and similar species, as well as compare time points such as E9.5 vs E12.5

Whole-Organ Imaging

Image whole mice (or any species) organs up to 15/20mm (greater, sample dependent) allowing for imaging of these denser areas to be visualised ex-Vivo or in-Situ. Combine HREM with multi-fluoresce for experimental staining and exploration.

  • 3D Kidney, Brain, Lung, Liver and Spleen in one high resolution dataset

  • Understand spatial relationships that 2D slices cannot visually explain

Cardiac & Vascular Imaging

Image whole cardiac structures with close to histology resolution, with the advantage of 3D analysis.

  • Measure chamber volumes with accuracy and segment manually as well as wall thickness and valve morphology

  • Image the heart within the structure at higher resolution with scanning

  • Ideal for the study of congenital heart defects, angiogenesis and more heart applications

Craniofacial

Craniofacial imaging requires imaging of extremely dense structures including bone, HREM handles bone extremely well. For imaging head, face, jaw and brain regions in smaller models such as mice.

  • Captures hard and soft tissue together with bone, cartilage, skin, nerves, and vessels

  • Ideal for cleft palette, craniosynostosis and further development studies

  • Quantitative measurements for jaw angles, sinus volumes and brain/skull alignment

Plant Science & Agricultural Research

Plant structures often prove difficult to image, due to the density, HREM offers a solution for this. With clear, even contrast on samples up to 20mm (more, sample dependent) allowing full reconstruction of developing plants, seeds, and roots.

  • HREM has been used to visualise seed structure, fruit peel oil cavities, stem vascular bundles and growing in this sector

  • Easily compare mutants and wild type

  • Ideal for quantitative studies for cavity density, wall thickness or overall morphology

Insects (Drosophila & Beyond)

Image the complex structures of inspects such as drosophila (fruit fly) for imaging of both cuticle and soft tissue without registration.

  • Ideal for imaging mutants, developmental stages and transgenic lines

  • No need for dissection, image whole mount at resolutions down to 1 micron with clear contrast

OHREM for You  

Our instruments the MICRO and ULTRA systems allow imaging of these applications with streamlined benefits and high resolution. All integrated into an easy to use package for vast applications wether you’re a lab or facility, get started with HREM by contacting us.

Don’t see your application? Get in touch and we will help determine if HREM is right for you.

Zebrafish embryo imaged with HREM, showing multiple cross-sectional views revealing internal morphology at micron-scale resolution.

Contact our High-Resolution Episcopic Microscopy (HREM) Experts

Request a quote or a meeting to discuss the Optical HREM Micro instrument using the form.

Contact Us 

Intech House

34-35 Wilbury Way

SG4 0TW

Hitchin

Hertfordshire 

United Kingdom

  • Youtube
  • Flickr
  • Instagram
  • LinkedIn
  • Twitter

© 2025 by Indigo Scientific.

bottom of page