What is 3D Optical High-Resolution Episcopic Microscopy (HREM)?

3D Optical HREM is a block-face imaging technique that captures high-resolution images of a sample as it is sectioned. Each slice is imaged at the block surface and stacked into a 3D reconstruction with minimal distortion.

How does HREM differ from confocal and light-sheet microscopy?

HREM physically sections the sample and images the freshly cut surface, producing aligned, high-contrast slices. Confocal and light-sheet rely on optical sectioning and perform best on fluorescent or transparent samples, while HREM is suited to dense or opaque tissue.

What sample types are suitable for HREM imaging?

HREM works well with embryos, small organs, tissue blocks, plant material and other dense or opaque specimens. It is especially useful for samples that confocal or light-sheet microscopes struggle to image.

What resolution can HREM imaging achieve?

HREM typically achieves 1–8 µm voxel size. X–Y resolution is often higher than Z resolution.

What are the advantages of HREM over traditional sectioning methods?

HREM avoids distortion by imaging the block face directly, producing aligned, high-contrast slices. This enables cleaner 3D reconstructions, less manual handling and faster workflow compared to manual sectioning.

How long does a typical HREM imaging session take?

Imaging usually runs at 6–7 seconds per section. Total time depends on section thickness and sample depth; for example, 1 µm sections take around 2 hours per mm of tissue. Larger embryos can take several hours. Multiple blocks can be imaged in one run to improve efficiency.

What sample preparation is required for HREM?

Samples must be fixed, dehydrated and resin-embedded to allow clean sectioning. The polymerised block provides stability for consistent slicing and high-contrast block-face images.

What software is used for 3D reconstruction and analysis?

HREM datasets can be processed in ImageJ/Fiji, Imaris, Amira and other volume-rendering tools for 3D reconstruction, segmentation and measurement.

Do you supply HREM systems worldwide?

Yes. We supply HREM systems worldwide and offer remote support, installation guidance, servicing and customised configurations with international shipping.

What support or training is provided after installation?

We provide ongoing support, remote assistance, software help, troubleshooting and training on system operation, sample preparation and data handling.

How do I request a quotation or discuss a custom HREM setup?

Contact us via form, phone or email with your application, sample type and imaging requirements, and we will prepare a suitable configuration and quotation.

What are the limitations of HREM imaging?

HREM requires resin embedding and physical sectioning, so it is destructive and not suitable for live samples. Fluorescence cannot be captured directly, datasets can be large and calcified or very large samples may need extra preparation.

Products / High-Resolution Episcopic Microscopy (HREM)

High-Resolution Episcopic Microscopy (HREM)

High-Resolution 3D Imaging for Biological Structure

High-Resolution Episcopic Microscopy (HREM) volumetric imaging systems for structural analysis of samples in 2D and 3D

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High-Resolution Episcopic Microscopy (HREM) Micro 3D Imaging System Showing a Mouse Embryo Being Imaged on Monitor.

3D reconstruction of a mouse heart imaged using High-Resolution Episcopic Microscopy (HREM), showing detailed internal anatomy as the structure rotates.

Volumetric rendering of a cardiac sample captured using Optical HREM

What is High-Resolution Episcopic Microscopy (HREM)?

High-Resolution Episcopic Microscopy (HREM) is a 3D imaging technique for visualising samples ranging from 1-30mm. Resin mounted samples are stained, then sectioned repeatedly with the remaining block face imaged, creating high-resolution 3D stacks at 1–8-micron voxel resolution.

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High-Resolution Episcopic Microscopy (HREM) Workflow

1. Sample Preparation

Samples are dissected, fixed, dehydrated and stained, before embedding in resin according to the established High-Resolution Episcopic Microscopy (HREM) protocols. Resin embedding preserves three-dimensional morphology, which allows for intrinsic registration and structural integrity.

Sample preparation for High-Resolution Episcopic Microscopy showing a stained specimen embedded in resin prior to serial sectioning

2. Sectioning

Resin blocks are sectioned at a consistent thickness of 1-5 microns depending on resolution requirements. HREM then images the exposed surface before the next section is removed. Sections may be optionally recovered via the extraction system or manually for downstream analysis.

Serial sectioning in High-Resolution Episcopic Microscopy illustrating thin section removal from a resin block

3. Imaging

The exposed block surface is captured at each sectioning step, using a HREM imaging setup. Optical sectioning and scanning approaches may be integrated to enhance contrast or suppress out of focus information.

Block-face imaging step in HREM capturing the exposed resin surface during serial sectioning

4. Reconstruction & Analysis

Sequential images are exported as 2D images (e.g tiff), allowing direct reconstruction into 3D volumetric datasets without complex post-acquisition registration. Data can be segmented and quantified using platforms such as Imalytics Preclinical, Imaris, Dragonfly or Fiji.

3D reconstruction from sequential HREM block-face images forming a volumetric dataset

Advantages of High-Resolution Episcopic Microscopy (HREM)

High-Resolution Episcopic Microscopy (HREM) as a serial block-face 3D imaging technique offers several practical advantages to other volumetric imaging methods. Because imaging occurs prior to section removal, geometric fidelity is preserved without the requirement for tissue clearing, manual slide alignment or complex post-acquisition registration.

HREM image of a mouse embryo sample alongside its corresponding 2D block-face section.

Whole mouse embryo captured using Optical HREM system, shown with corresponding 2D block-face section.

Intrinsic Alignment

HREM produces inherently registered stacks by imaging the block surface, reducing registration complexity and preserving spatial accuracy.

Large Volume with Micro Detail

Samples up to ~25mm can be imaged while maintaining micron-scale resolution, with scanning extending field of view possibilities.

High Contrast in Dense or Opaque Samples

Surface-based imaging enables consistent capture of bone, pigmented tissue, opaque tissue and dense organs which may be limited by optical penetration limits on other volumetric techniques.

True Volumetric Resolution

Consistent section 1-5 micron section thickness allows for accurate 3D measurements, suitable for morphometric analysis.

No Tissue Clearing Required

As imaging is performed directly on the block surface, optical clearing is not necessary, which reduces preparation complexity and other complications.

Quantitative Stability

HREM is suitable for volumetric measurement, surface area quantification, branching analysis and phenotypic screening due to the repeatability, resolution and scale.

Flexibility for a Range of Samples

High Resolution Episcopic Microscopy is less impacted by optical penetration depth than other volumetric techniques, as imaging is performed directly on the resin block surface. This produces reliable three-dimensional imaging of structures including bone, calcified structures and pigmented tissue with complex samples with mixed density producing high contrast.

HREM supports imaging across a wide range of biological samples, including mixed density tissues within a sample.

Suitable for bone, calcified structures and pigmented tissues
Maintains contrast across soft and dense tissue
Enables imaging of intact samples such as whole
Compatible with samples up to 25mm in a single acquisition, with larger areas possible with scanning

Mouse Embryos

Drosophila

Fruit & Plant Samples

Barley

Zebrafish

Other Fish Samples

Embryonic Hearts

Reproductive Systems

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High Resolution for All Tissue and Sample Types

HREM typically operates within the voxel size range between 1-8 microns, with section thickness defining the Z resolution, enabling accurate 3D measurements and reliable structural reconstruction.

At these resolutions, fine structures can be visualised and quantified/segmented such as small vessels, branching networks, nerve structures and tissue boundaries. Unlike conventional imaging approaches where resolution can decrease with sample size, HREM maintains resolution with scanning configurations.

1-8 Micron voxel resolution for detailed volumetric imaging
Defined axial resolution via physical section thickness
Scanning configurations for extended field of view at maintained resolution

HREM 3D embryonic mouse cross section captured with HREM morphology imaging system

High-resolution stitched Optical HREM Ultra image of a mouse section, revealing fine structural detail across the tissue.

Applications of High-Resolution Episcopic Microscopy (HREM)

HREM has been widely used in multiple disciplines and can be applied to a wide range of morphological studies. Imaging denser samples up to 25mm down to below 1mm with voxel sizes down to 1 micron. Most commonly, samples in the range of 1-12 mm are imaged for detailed structural analysis.

Mouse Embryos

HREM has been widely used to image full mouse embryos across all stages of development

Full 3D reconstruction of whole mouse embryos in high detail
Track developmental abnormalities across gestational stages
Quantify organ formation and spatial relationships

Chick Embryos

Large scale imaging of early vertebrate development
Assess segmentation, heart looping and organogenesis
Bridge developmental biology with anatomical analysis

Plant Samples/Seeds

3D imaging of seed structures and root development
Image vascular bundles, meristems and embryogenesis
Ideal for agricultural trait research and seed phenotyping

Small Animal Organs

Capture kidney, liver and lung in full 3D under 1 cm
Measure volume, surface area and branching networks

Mouse Hearts

HREM has aided mouse heart imaging at all stages.

Visualise intricate 3D cardiac structures and vasculature
Study congenital heart defects (CHD) and structural remodelling
Ideal for phenotyping mutant mouse lines

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Zebrafish
Drosophila (fruit flies)
Human biopsy samples
Nervous system/Brain imaging
Much more

HREM Applications

Publications

Simplified Imaging Workflow with HREM

High-Resolution Episcopic Microscopy (HREM) generates standard 2D image stacks straight from the system, enabling direct 2D and 3D analysis workflows. Files are typically exported in supported formats such as TIF, ensuring compatibility with open source and commercial image analysis packages.

HREM data can be manually or automatically segmented for volumetric reconstruction, morphometric measurement and quantitative analysis. Software such as Fiji, Dragonfly, Imaris and Imalytics Preclinical can be used without requiring further proprietary software for image handling.

Support of standard and widely accessible formats (e.g. TIF, PNG)
Compatible with common 3D analysis platforms
No vendor-locked processing pipeline
Support segmentation, rendering and quantitative measurements

2D Mouse Heart Sections

3D Mouse Heart Reconstruction

Want to Visualise HREM?

Want to view a HREM 3D sample, crop and export use our 3D viewer with a dedicated embryonic mouse sample captured with High-Resolution Episcopic Microscopy.

HREM 3D Viewer

Optical HREM Ultra System Imaging an Embryonic Sample

Dr Duncan Sparrow

DPAG, University of Oxford

'We are extremely happy with the high quality 3D imaging of our samples. The OHREM system is very flexible, and fully upgradable. We initially only had funds for the single-channel model. However, when we got another grant 12 months later, able to upgrade our system to a 2-channel model with less than 24 hours downtime. The system is very reliable, with virtually no maintenance required. For example, we have used our machine 24/7 for months on end, without any repairs required. In the 2 years we have had the OHREM, we have achieved completely consistent data quality. Aftersales service is friendly, prompt and informative. '

Optical HREM Systems

We offer two main Optical HREM system solutions, available worldwide, offering flexibility in budget and in capture. Each system can achieve highly detailed 3D image stacks, while allowing the systems to be accessible to more.

Optical HREM Micro 3D block face imaging sstem, imaging mose embryo with 3D running

OHREM Micro

Micro OHREM Systems offer simple imaging of samples up to 25mm in FOV, featuring single shot optics.

Highlights

25 x 20 x 20 field of view
Simplistic single shot imaging
Smaller form factor, ideal for individual labs or for streamlined operations

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Optical HREM Ultra block face 3D imaging system imaging a mouse embryo with a 3D

OHREM Ultra

Ultra OHREM systems offer flexible imaging with XY scanning stages with various illumination and optical setups.

Highlights

Larger field of view, enabled with scanning
Choice of optics and configurations
Ideal for more demanding applications such as facilities

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HREM Products

Frequently asked questions

HREM samples can be imaged at 6–7 seconds per section, though this varies with section thickness and sample size. Approximate imaging speed per millimetre • 1 µm → 1000 sections → ~1 hr 57 mins • 2 µm → 500 sections → ~58 mins • 3 µm → 333 sections → ~39 mins • 4 µm → 250 sections → ~29 mins • 5 µm → 200 sections → ~23 mins • Real-world example timings • Embryonic mouse heart (E14–E16, ~1.5–2.0 mm deep) • 1 µm: 2.5–3.3 hrs • 2 µm: 1.3–1.9 hrs • 3 µm: 1.0–1.3 hrs • E10–E11 mouse embryo (small, ~4–6 mm deep) • 1 µm: 6.7–11.7 hrs • 2 µm: 3.3–7.0 hrs • 3 µm: 2.2–3.9 hrs • E14–E15 mouse embryo (larger, ~8–10 mm deep) • 1 µm: 13–19 hrs • 2 µm: 6.7–9.7 hrs • 3 µm: 4.4–6.5 hrs Time efficiencies can be achieved by combining samples into one block or by imaging multiple blocks in a single run using the Ultra system, which reduces sectioning overheads and allows the instrument to run unattended.

HREM is a block-face imaging technique, while confocal and light-sheet systems capture images through intact tissue. HREM physically sections the sample and images the freshly cut surface, producing perfectly aligned slices with high structural contrast. Confocal and light-sheet are excellent for fluorescent, transparent or cleared samples, but HREM is ideal for dense or opaque tissues and for capturing fine anatomical detail across larger volumes.

Contact our High-Resolution Episcopic Microscopy (HREM) Experts

Want to know more about HREM, ask for a quote or get questions answered. Contact us and we can help answer all your questions.

Phone:
+44(0) 1462633500

Email:
hello@indigo-scientific.co.uk