High-Resolution Episcopic Microscopy / Applications / Heart Imaging

3D Heart Imaging in Mouse and Embryos Using HREM

3D Imaging of Mouse Cardiovascular Systems at Micron Resolution

High-Resolution Episcopic Microscopy (HREM) provides detailed, gap-free 3D datasets of cardiac structures in mouse embryos, postnatal pups, adult mice, and chicken embryos at 1–6 micron voxel resolution. From early cardiac looping at E9.5 through to adult ventricular morphology, HREM delivers the structural clarity and quantitative precision required for cardiovascular research, congenital heart defect characterisation, and cardiac phenotyping in gene knockout models.

Mouse Heart in 3D Imaged with High-Resolution Episcopic Microscopy (HREM)

Mouse Heart 3D Credit: Dr. Aseel Abbad (University of Nottingham, UK)

Imaging Heart Development in Mouse and Embryo Models

High-Resolution Episcopic Microscopy (HREM) provides precise 3D datasets of cardiac structures in mouse and chicken embryos, with sample sizes ranging under 1mm up to 25mm.

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3D Heart Imaging in Small Models with HREM

High-Resolution Episcopic Microscopy is a block-face 3D imaging technique that produces complete, registered datasets of cardiac structures in small animal models, without section loss, compression artefacts, or the registration errors that affect conventional histology reconstructions.

HREM is particularly well suited to cardiac imaging because the heart's complex 3D architecture (interlocking chambers, thin-walled septa, valve leaflets, and vessel origins) cannot be reliably characterised from 2D sections alone. A complete volumetric dataset allows researchers to assess structural relationships, measure cavity volumes, and identify subtle morphological variants that would be missed or misclassified in conventional serial histology.

Whether you are studying embryonic mouse heart development across the E9.5–E18.5 morphogenesis window, characterising congenital heart defects (CHD) in knockout lines, or performing comparative cardiac anatomy in chicken embryo models, HREM provides the resolution and 3D context required.

3D reconstructed image of a mouse embryo heart captured using High-Resolution Episcopic Microscopy (HREM)

How High-Resolution Episcopic Microscopy Enhances 3D Heart Imaging

Multi

samples per run

High-throughput cardiac imaging

HREM supports multiple samples per imaging run using scanning stages, making it practical for knockout phenotyping trials and large cohort studies. Datasets are acquired consistently and are directly comparable across animals, reducing the operator variability that affects manual histology workflows.

360°

cardiac anatomy

Complete 3D cardiac anatomy

HREM resolves the full cardiac architecture including ventricular and atrial chambers, atrioventricular and semilunar valves, interventricular and interatrial septa, outflow tracts, and great vessel origins. Structures are captured in their correct spatial relationships, supporting accurate classification of complex congenital malformations.

quantitative
measurement

Quantitative volumetric analysis

Unlike optical methods that degrade with depth, HREM resolution is consistent across the entire z-depth of the sample, because each image is acquired from the freshly cut block face rather than through intervening tissue.

JB-4

resin embedded

Consistent, reproducible contrast

HREM produces contrast that is consistent across samples and acquisition runs. Without the variability of immunostaining, datasets from different animals, and timepoints can be compared directly.

Benefits of HREM for Cardiac Imaging

Optical resolution to 1µm Resolves vessel walls, valve leaflet margins, and trabecular architecture at a level of detail not achievable with micro-CT on unstained tissue.
Dense tissue compatibility Myocardial tissue, vessel walls, and partially mineralised structures in older specimens are all imaged with consistent contrast — no clearing required, no tissue-dependent degradation of image quality.
Repeatable and standardised The block-face acquisition method is inherently reproducible. Without clearing or staining variability, results are consistent across operators, runs, and timepoints — making HREM suitable for regulated preclinical workflows.
2D and 3D from a single acquisition Every HREM run produces both a complete stack of 2D section images and the raw data for 3D reconstruction. Researchers can review individual sections for histological assessment and generate 3D models from the same dataset — no second acquisition needed.

3D Embryonic mouse structure with plane views

Applications of HREM in Cardiac Research

HREM allows researchers study heart development and disease in animal models.

Heart Development in Mice
- HREM enables detailed 3D imaging of heart development in mice, offering critical insights into congenital heart.
Mice Embryo Cardiac Imaging
- Imaging of cardiac imaging the full embryo, making it possible to study the heart at various stages of embryonic development (E9.5–E14.5).
Chicken Embryo Heart Imaging
- Effective for imaging chicken embryos, providing valuable data for comparative studies in cardiac research.
Larger Samples
- HREM can be used to image denser larger cardiac systems, such as pups, supporting small animal heart imaging and 3D tissue morphology analysis.