Applications / Serial Block Face Imaging

Serial Block-Face Imaging for 3D Reconstruction

High-Resolution 3D Imaging for Complex Biological Structures

Generate inherently aligned 2D image stacks through serial block-face imaging, enabling accurate 3D volumetric reconstruction.

Optical HREM Ultra system performing serial block-face imaging on a resin-embedded biological sample.

Block-face image of a mouse torso displayed alongside its reconstructed 3D volumetric model.

What Is Serial Block-Face Imaging?

Serial block-face imaging (SBF-imaging) is a volumetric imaging technique in which a specimen, typically embedded in resin or other mediums, and the exposed surface is imaged after each cut. This results in evenly displaced, inherently aligned 2D image stacks that can be reconstructed into 3D volumetric datasets.

Unlike traditional histology, which requires manual mounting and alignment of individual sections, serial block face imaging repeatedly images the blocks surface.

Serial Block-Face Imaging Workflow

Step 1 — Sample Preparation and Embedding

The specimen is fixed, dehydrated, and embedded in resin (or another suitable medium) following a block-face preparation protocol. Once polymerised, the block is ready for imaging and sectioning.

Illustration of a mouse specimen being embedded in resin for serial block-face imaging.

Step 2 — Serial Sectioning

The embedded sample is physically sectioned at controlled intervals, typically 1–5 µm, using a bespoke setup. Sections are removed sequentially, and retained sections may be recovered if required.

Diagram showing a mouse specimen being physically sectioned during serial block-face imaging.

Step 3 — Block-Face Imaging

After each cut, the newly exposed block surface is imaged using optical systems. Scanning can be used to increase field of view, resolution, or to capture multiple specimens within a single block.

Close-up of the exposed block surface being optically imaged during serial block-face acquisition.

Step 4 — 3D Reconstruction

The resulting image stack forms an inherently aligned dataset that can be reconstructed into a 3D volumetric model for visualisation and quantitative analysis.

Illustration of a reconstructed 3D volumetric dataset generated from aligned block-face image stacks.

Types of Serial Block-Face Imaging

Serial block-face imaging encompasses a range of techniques, from serial block-face scanning electron microscopy (SBF-SEM), which is typically used for ultrastructural imaging at very high resolution, to optical serial block-face methods such as High-Resolution Episcopic Microscopy (HREM), which are suited to larger biological specimens ranging approximately from 1 mm up to 30 mm, sometimes greater with experimentation.

OHREM Ultra system showing microtome blade sectioning a resin block while optically imaging a mouse specimen with scanning.

Types of Serial Block-Face Imaging

Serial block-face imaging is widely used in applications that require high-resolution volumetric analysis of complex biological structures. The technique is particularly suited to studies where detailed structural information, consistent section alignment and accurate 3D reconstruction are essential.

Common applications include:

Structural analysis of complex biological tissues
Developmental biology studies, including embryonic and organ development
Zebrafish imaging for whole-organism morphological reconstruction
Mouse embryo imaging for developmental and phenotyping workflows
Congenital defect analysis and anatomical investigation
Genetic phenotyping studies in preclinical research
Organ morphology and anatomical reconstruction

HREM image of an embryonic mouse heart showing ventricular structures in cross section.

Advantages of Optical Serial Block Face Imaging

Optical serial block-face imaging produces intrinsically aligned image stacks, eliminating the need for complex post-acquisition registration and reducing alignment artefacts commonly associated with traditional histology.

Because the specimen is physically sectioned during imaging, consistent data can be acquired throughout dense tissue volumes without depth-related optical distortion. This enables reliable imaging of larger samples and supports accurate quantitative analysis in three dimensions.

Serial Block Face Imaging vs Other 3D Imaging Techniques

Serial Block Face Imaging

Optical serial block-face imaging, such as HREM, combines physical sectioning with surface imaging to generate intrinsically aligned volumetric datasets. The technique supports micron-scale resolution across whole biological specimens and is commonly used for developmental and phenotyping studies.

Micro CT

Micro-CT uses X-ray attenuation to reconstruct a sample in 3D by rotating it between an X-ray source and detector. It is a non-destructive technique and is particularly suited to mineralised or skeletal structures, as well as larger specimens from several millimetres up to centimetre scale. Soft tissue contrast often requires additional staining.

Light Sheet Microscopy

Light sheet microscopy optically sections a sample using a thin sheet of light, most commonly for fluorescence imaging. It is widely used in developmental biology and often requires optical clearing to achieve deeper penetration. Image quality is dependent on labelling strategy and tissue transparency.

Histology Techniques

Traditional histology relies on manual sectioning and slide mounting to generate thin tissue sections. While extremely high resolution in 2D, reconstruction into 3D requires alignment of individual sections and can be labour intensive.

Illustration of traditional histology showing thin tissue sections mounted on slides for 2D analysis.

Optical Serial Block-Face Imaging with HREM

Optical serial block-face imaging can be implemented using High-Resolution Episcopic Microscopy (HREM). By combining precision sectioning with surface imaging, HREM generates intrinsically aligned volumetric datasets suited to developmental biology, phenotyping, and structural morphology studies.

Indigo Scientific’s Optical HREM (OHREM) systems are designed for micron-scale block-face imaging of whole specimens and isolated organs, supporting accurate 3D reconstruction across a range of biological and agricultural samples.

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HREM Micro system performing optical serial block-face imaging on a resin-embedded biological specimen.