High-Resolution Episcopic Microscopy / Applications / Mice and Zebrafish
3D Imaging of Mouse Embryos,
Pups & Zebrafish
Gap-free, histology-quality 3D datasets at micron resolution featuring no clearing, no distortion, no sectioning artefacts. HREM systems for developmental biology, phenotyping and cardiovascular research, supplied worldwide.
Why choose HREM
vs micro-CT, light sheet, OPT & serial histology
Mouse embryo & pup imaging
Heart, brain, kidney, gut for whole specimens and organ imaging
Zebrafish 3D imaging
Larvae, juveniles and adult organs for full developmental imaging range
Research applications
Cardiovascular, neuroanatomy and phenotyping screens
HIGH-RESOLUTION EPISCOPIC MICROSCOPY - MICE & ZEBRAFISH
Overview of 3D imaging of mouse and zebrafish samples
High-Resolution Episcopic Microscopy (HREM) captures mouse and zebrafish samples across the full developmental range, from sub-millimetre embryos to adult whole organs. Indigo Scientific HREM systems produce large, high-quality image stacks at high throughput, with no requirement for sample clearing and no distortion introduced to the block face during acquisition.
This technique supports both whole 2D section review and complete 3D reconstruction from a single dataset, making it practical for developmental biology, phenotyping screens and structural research within the same workflow.
Image stacks are inherently aligned from acquisition, ready for immediate 3D morphological reconstruction and quantitative analysis, with no computational alignment step required.
HREM VS MICRO-CT, LIGHT SHEET, OPT AND SERIAL HISTOLOGY
Why choose HREM over other 3D imaging techniques
Researchers comparing 3D imaging methods for mouse and zebrafish work often evaluate HREM alongside micro-CT, light sheet microscopy, optical projection tomography (OPT) and serial histology. Here is where HREM stands apart.
0
gaps
Inherently aligned image stacks with no registration step
Serial block-face imaging produces datasets perfectly registered by acquisition. There is no computational alignment step required, and none of the cumulative registration errors that affect histological section stacks reconstructed post hoc.
No
clearing
No sample clearing required
Unlike light sheet or OPT, HREM does not require optical clearing — a major advantage for dense tissue, mineralised structures, or specimens where the clearing process itself introduces distortion or shrinkage artefacts.
Full
soft tissue
Excellent soft tissue contrast throughout
Histology-like contrast enables clear visualisation of organs, vasculature and fine tissue boundaries, detail that micro-CT alone often cannot resolve in soft tissue without contrast agents.
3D
imaging
Economical high-resolution 3D reconstruction
HREM delivers high-resolution structural detail, consistent contrast and accurate 3D reconstruction of small biological specimens, while remaining economical compared to micro-CT or light sheet platforms.
TECHNICAL SPECIFICATIONS
Why choose HREM over other 3D imaging techniques
SAMPLE SIZE RANGE
<1mm -25mm
Broad sample size range
From early mouse embryos at E9.5 through to postnatal pups and adult zebrafish organs. Larger samples can be accommodated on reques
VOXEL SIZE
1-8 microns
Fine structural detection
Voxel sizes of 1–6 microns enable identification of subtle anatomical changes relevant to phenotyping and disease studies, at a resolution micro-CT and MRI cannot match for soft tissue.
IMAGE RESOLUTION
20+MP
High resolution throughout the volume
Unlike traditional optical methods that degrade with depth, resolution is maintained across the entire z-depth because each image is acquired at the block face, not through intervening tissue.
DEVELOPMENTAL BIOLOGY & PHENOTYPING
Applications in developmental biology and phenotyping
HREM is applied across a wide range of studies in mouse and zebrafish models, including:
Neuroanatomy and brain imaging
Image whole brains for detailed analysis of tissue architecture and structural organisation, without the distortion introduced by optical clearing methods required by light sheet or OPT.
Knockout and phenotyping screens
HREM is routinely used in large-scale phenotyping programmes requiring rapid, standardised 3D characterisation. A single acquisition can replace weeks of serial histology. Multi-sample stages allow several embryos to be imaged in a single block, significantly increasing throughput for screen-scale work.
Whole organ morphology
Image individual organs including kidney, lung, liver, and gut, for anatomical and developmental analysis. Particularly well suited for knockout models that require complete 3D context to characterise accurately.
Cardiovascular imaging
Visualise whole hearts in both 2D sections and fully reconstructed 3D models. HREM resolves chamber morphology, valve structures, septal anatomy and outflow tract alignment enabling classification of congenital defects including VSD, AVSD and transposition of the great arteries. Ventricular volumes can be quantified directly.
MOUSE EMBRYO & PUP IMAGING
3D Mouse Embryo and Mouse Pups in Full
High-Resolution Episcopic Microscopy is widely used to image individual organs dissected from mouse embryos and pups, as well as whole intact specimens. HREM systems are particularly well suited to capturing detailed datasets of the heart, kidney, brain and gut for structural and developmental analysis, producing data that supports both qualitative assessment and quantitative volumetric measurement from the same acquisition.
Whether you are characterising a knockout model, running a developmental biology study or conducting cardiovascular phenotyping, HREM provides a single imaging platform for the full analysis pipeline.
ZEBRAFISH 3D IMAGING
Zebrafish Imaging in 3D
Zebrafish is one of the most widely used vertebrate model organisms in developmental biology and genetics, and HREM, though not common, can image across its full developmental range. Zebrafish larvae, juveniles and dissected adult organs can all be imaged without clearing, an important advantage for researchers working with denser tissue or mineralised structures where optical clearing methods become unreliable.
Chick embryos, catfish and other aquatic species at comparable size ranges are also compatible with HREM imaging.
Frequently asked questions
What sample sizes can HREM image for mouse and zebrafish work?
Sample sizes from under 1mm up to 25mm are covered as standard, accommodating early mouse embryos at E9.5 (approx. 2–3mm crown-rump length) through to postnatal pups and adult zebrafish organs. Larger samples can be accommodated on request. Contact us with your specific sample size requirements.
Does HREM require optical clearing?
No — HREM does not require optical clearing. This is a significant advantage over light sheet microscopy and OPT, particularly for dense tissue, mineralised structures, or samples where the clearing process introduces distortion or shrinkage artefacts. Standard sample preparation for HREM does not require the specialist reagents or handling that clearing protocols demand.
Does HREM require optical clearing?
HREM offers significantly superior soft tissue contrast and finer voxel resolution (1–6 microns) compared to typical micro-CT, without requiring contrast agents. Micro-CT provides excellent bone and mineralised tissue contrast but struggles with soft tissue differentiation at this scale. HREM is also more economical for high-resolution 3D reconstruction of small specimens. Many research groups use both techniques depending on the tissue type and research question. Learn more here.
Can HREM be used for cardiovascular phenotyping in mouse embryos?
Yes — HREM is widely used for cardiovascular phenotyping. It resolves chamber morphology, valve structures, septal anatomy and outflow tract alignment with the clarity needed to classify congenital heart defects such as ventricular septal defects (VSD), atrioventricular septal defects (AVSD) and transposition of the great arteries. Ventricular volumes can be quantified directly from the 3D dataset. See our cardiovascular imaging page for more detail.
What other species can be imaged with HREM besides mice and zebrafish?
Chick embryos, catfish and other aquatic or small vertebrate species at comparable size ranges are also compatible with HREM imaging. The key factor is sample size, specimens from under 1mm to 25mm are accommodated as standard. Contact us to discuss compatibility with your specific model organism.
Indigo Scientific - HREM Team
Based in Hertfordshire, UK. Systems shipped and supported worldwide.