High-Resolution Episcopic Microscopy (HREM) / Applications

High-Resolution Episcopic Microscopy (HREM) Applications

Complete 3D imaging of biological samples at histological resolution

Various HREM samples showcasing applications

Flexible 3D Imaging at Micron Scale

High-Resolution Episcopic Microscopy is a powerful 3D imaging technique suited to a wide range of biological and material samples. By imaging embedded block faces sequentially, HREM produces complete, gap-free volumetric datasets at histological resolution, without the time, cost, or tissue loss of traditional serial sectioning.

HREM System Applications

Applications commonly, but not limited to, for HREM imaging. Perform 3D imaging of mouse hearts, barley, whole embryos and more with this cost effective 3D imaging technique. Click here to view HREM examples such as 3D or 2D images.

Developmental Biology

Whole Embryo Imaging

Mouse and zebrafish embryos are among the most demanding subjects in developmental biology. They require whole-sample 3D context to properly characterise structural phenotypes. HREM captures entire embryos at each developmental stage in a single acquisition run, producing complete volumetric datasets that replace hundreds of histology slides.

Mouse embryo staging from E9.5 through E18.5
Zebrafish whole-body imaging at key developmental stages
Neural tube closure defects, craniofacial anomalies, laterality
Quantitative organ volume comparison across cohorts
Retrospective digital re-sectioning in any plane

Drosophila & Invertebrate Imaging

Drosophila melanogaster is one of the most widely used genetic model organisms, but 3D phenotypic characterisation of adult or larval flies is poorly served by existing imaging methods. HREM resolves internal anatomy at the resolution needed to detect subtle morphological changes in genetic screens.

Also applicable to other common invertebrate models including C. elegans, beetle larvae, and moth pupae used in evo-devo research.

Adult fly nervous system, gut, and musculature in 3D
Screen-compatible throughput with multi-sample scanning stages

View Drosophila image examples

Fluorescence / Expanding

Fluorescence Block-Face Imaging with Structured Illumination

Traditional HREM relies on block staining of JB-4-embedded tissue to generate contrast, which limits to a single broadband signal. By combining block-face imaging with structured illumination, it becomes possible to acquire specific fluorescence channels from the block face, opening up targeted labelling strategies that standard episcopic microscopy cannot access.

GFP and fluorescent reporter imaging in transgenic mouse and zebrafish lines
Targeted antibody or dye labelling prior to embedding, captured at block face
Structured illumination rejection of sub-surface resin background
Co-registered fluorescence and autofluorescence channels in a single dataset

Enquire about fluorescence imaging

Cardiovascular

Heart and Cardiovascular Research

Congenital heart defects are among the most common phenotypes in developmental genetics screens, yet their characterisation by conventional histology is notoriously time-consuming and prone to section loss at critical structures. HREM provides complete 3D cardiac datasets of chambers, valves, septa, and outflow tracts whith-in their correct anatomical context.

Ventricular septal defect (VSD) detection and classification
Valve morphology
Outflow tract alignment and great vessel relationships
Ventricular volume quantification for functional inference
Compatible with mouse, rat, and zebrafish cardiac models

Neuroscience & Brain Imaging

Fixed brain tissue imaging represents a growing application area for HREM. Where optical clearing methods require extensive sample preparation and may introduce distortion, HREM on embedded tissue preserves structural integrity across the full sample volume.

Whole rodent brain sectioning and 3D reconstruction

Method

Serial Block-Face Imaging with Resin

Perform block face imaging to create high detail 3D data with resin.

Gap-free image stacks — every section captured
No registration errors between adjacent sections
Consistent autofluorescent contrast without staining variability
Section thickness adjustable from ~1µm upward

Agricultural & Plant Samples

Plant tissue presents unique imaging challenges with complex 3D architecture, soft and hard tissue mixed within the same sample, and structures too large for electron microscopy but requiring more detail than X-ray CT. HREM fills this gap, offering improved soft tissue contrast for plant material at a competetive cost.

Barley and wheat grain internal structure and filling
Root architecture and morphology in 3D
Citrus and fruit peel microstructure

Organoids & 3D Culture Models

Organoids sit in a resolution and size range that suits HREM particularly well, too large and complex for confocal whole-mount imaging once mature, but requiring micron-level detail. HREM produces complete volumetric datasets of embedded organoids, enabling internal architecture assessment that surface imaging cannot achieve.

Intestinal, brain, and kidney organoid internal architecture

Enquire about organoid imaging

HREM Publications

Multi-fluorescence high-resolution episcopic microscopy (MF-HREM) for three dimensional imaging of adult murine organs.

Claire Walsh, Natalie Holroyd, Eoin Finnerty, Sean G. Ryan, Paul W. Sweeney, Rebecca J. Shipley, Simon Walker-Samuel

High-Resolution Episcopic Microscopy (HREM) Applications

Flexible 3D Imaging at Micron Scale

HREM System Applications

Whole Embryo Imaging

Drosophila & Invertebrate Imaging

Fluorescence Block-Face Imaging with Structured Illumination

Heart and Cardiovascular Research

Neuroscience & Brain Imaging

Serial Block-Face Imaging with Resin

Agricultural & Plant Samples

Organoids & 3D Culture Models

HREM Publications

Multi-fluorescence high-resolution episcopic microscopy (MF-HREM) for three dimensional imaging of adult murine organs.

High‐resolution episcopic microscopy enables three‐dimensional visualization of plant morphology and development

Cellular and morphological characterization of blastoderms from freshly laid broiler eggs.

A predictive model of asymmetric morphogenesis from 3D reconstructions of mouse heart looping dynamics.

Morphology, topology and dimensions of the heart and arteries of genetically normal and mutant mouse embryos at stages S21-S23.

The independence of the infundibular building blocks in the setting of double-outlet right ventricle.

High-resolution Episcopic Microscopy (HREM) - Simple and Robust Protocols for Processing and Visualizing Organic Materials.

Key Questions Relating to Left Ventricular Noncompaction Cardiomyopathy: Is the Emperor Still Wearing Any Clothes?

A staging system for correct phenotype interpretation of mouse embryos harvested on embryonic day 14 (E14.5).

Highly variable penetrance of abnormal phenotypes in embryonic lethal knockout mice.

Temporally Distinct Six2-Positive Second Heart Field Progenitors Regulate Mammalian Heart

ASPP2 deficiency causes features of 1q41q42 microdeletion syndrome.

High-throughput discovery of novel developmental phenotypes.

Insights regarding the normal and abnormal formation of the atrial and ventricular septal structures.

Development and Morphology of the Ventricular Outflow Tracts.

Morphogenesis of myocardial trabeculae in the mouse embryo.

Comparing homologous microscopic sections from multiple embryos using HREM.

Genetic dissection of Down syndrome- associated congenital heart defects using a new mouse mapping panel.

Clarification of mammalian cloacal morphogenesis using high-resolution episcopic microscopy.

The anatomy and development of normal and abnormal coronary arteries.

Clarifying the morphology of the ostium primum defect.

Postmortem high-resolution episcopic microscopy (HREM) of small human fetal hearts.

iASPP, a previously unidentified regulator of desmosomes, prevents arrhythmogenic right ventricular cardiomyopathy (ARVC)-induced sudden death.

The problems that exist when considering the anatomic variability between the channels that permit interventricular shunting.

The anatomy and development of the cardiac valves.

FGF10 promotes regional foetal cardiomyocyte proliferation and adult cardiomyocyte cell-cycle re-entry.

High-resolution episcopic microscopy (HREM): a tool for visualizing skin biopsies.

Tbx1 coordinates addition of posterior second heart field progenitor cells to the arterial and venous poles of the heart.

Phenotyping structural abnormalities in mouse embryos using high-resolution episcopic microscopy.

The development of septation in the four-chambered heart.

What is aortic overriding?

Cor triatriatum or divided atriums: which approach provides the better understanding?

Abnormal cardiac formation in hypertrophic cardiomyopathy: fractal analysis of trabeculae and preclinical gene expression.

A coming of age: advanced imaging technologies for characterising the developing mouse.

Tetralogy of Fallot: nosological, morphological, and morphogenetic considerations.

Hypoxic regulation of hand1 controls the fetal-neonatal switch in cardiac metabolism.

A chick embryo with a yet unclassified type of cephalothoracopagus malformation and a hypothesis for explaining its genesis.

Quantification of left ventricular trabeculae using fractal analysis.

Insights from cardiac development relevant to congenital defects and adult clinical anatomy.

Clarification of the identity of the mammalian fifth pharyngeal arch artery.

Defects in the oval fossa: morphologic variations and impact on transcatheter closure.

Lineage tree for the venous pole of the heart: clonal analysis clarifies controversial genealogy based on genetic tracing.

Normal and abnormal development of the intrapericardial arterial trunks in humans and mice.

Episcopic three-dimensional imaging of embryos.

Generation of volume data by episcopic three- dimensional imaging of embryos.

Embedding embryos for episcopic fluorescence image capturing (EFIC).

Comparison of ex-vivo high-resolution episcopic microscopy with in-vivo four-dimensional high- resolution transvaginal sonography of the first-trimester fetal heart.

Imaging heart development using high-resolution episcopic microscopy.

Three-dimensional and molecular analysis of the arterial pole of the developing human heart.

Sequential Binding of MEIS1 and NKX2-5 on the Popdc2 Gene: A Mechanism for Spatiotemporal Regulation of Enhancers during Cardiogenesis.

High-resolution episcopic microscopy (HREM): a useful technique for research in wound care.

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