3D Heart Imaging in Mouse
Embryos & Animal Models

HREM provides high resolution, consistent contrast and complete 3D imaging of the cardiac architecture in small animal models, at a level of detail and reproducibility not achievable with conventional histology or micro-CT. The heart's complex 3D structure (interlocking chambers, thin septa, valve leaflets) requires volumetric data to be reliably characterised. HREM produces a registered, gap-free dataset from which both 2D sections and 3D reconstructions can be derived. Resolution to 1µm resolves structures such as the membranous ventricular septum and valve leaflet margins that micro-CT cannot distinguish in unstained tissue.

Yes, HREM covers the complete E9.5–E18.5 mouse embryo developmental window as standard, from early cardiac looping and chamber formation through to mature four-chamber morphology in late-stage embryos. It also accommodates postnatal pups and adult mice for cardiac imaging. Chicken embryo cardiovascular systems at multiple HH stages are also compatible. Contact us with your specific developmental stage and sample size for confirmation.

HREM offers significantly superior soft tissue contrast for cardiac imaging compared to micro-CT, without contrast agents. Micro-CT excels for bone and mineralised structures but struggles to resolve thin soft tissue structures (valve leaflets, membranous septum, trabecular architecture) in unstained cardiac specimens. HREM provides 1µm resolution with histology-quality contrast at a cost point that is more accessible than high-resolution micro-CT for cardiac applications. Many cardiovascular research groups use both techniques: micro-CT for bone/vessel structure, HREM for soft tissue cardiac detail.

Yes — HREM is widely used as the gold-standard imaging method for congenital heart defect (CHD) characterisation in mouse knockout lines. Defects including ventricular septal defects (VSD), atrioventricular septal defects (AVSD), transposition of the great arteries (TGA), double outlet right ventricle (DORV) and persistent truncus arteriosus can all be reliably classified from 3D HREM datasets. The 3D spatial context is essential, many of these defects cannot be unambiguously classified from 2D histological sections, where the apparent anatomy depends entirely on the plane of section.

Yes, HREM is routinely used in large-scale cardiac phenotyping programmes. Multi-sample scanning stages allow several embryos to be embedded and imaged in a single block, significantly increasing throughput. The inherently reproducible block-face method means datasets are directly comparable across animals within a cohort without operator-dependent staining variability. A single HREM acquisition run can replace weeks of serial histology sectioning for cardiac phenotyping purposes.

Yes, HREM is not limited to mouse heart imaging. Chicken embryos, zebrafish, rat embryos and other small vertebrate species are all compatible within the standard sample size range (under 1mm to 25mm). Other organs including brain, kidney, liver, lung and gut are regularly imaged using HREM. OHREM systems extend specimen size beyond 25mm for larger biological material. See our mice and zebrafish application page and all HREM applications for further detail.

Yes, Indigo Scientific supplies HREM and OHREM systems worldwide to cardiovascular research groups, developmental biology departments, core imaging facilities and pharmaceutical preclinical teams. We work with groups across Europe, North America, Asia and beyond. Contact us to discuss your cardiac imaging requirements, specimen types and throughput needs, we will advise on the right system and support arrangement for your location.