High-Resolution Episcopic Microscopy / Applications / Agricultural Imaging
3D Plant & Crop
Imaging at Micron Scale
High-Resolution Episcopic Microscopy (HREM) creates perfectly aligned 3D morphology stacks of agricultural samples from barley grain to citrus fruit, with no sample clearing required
1 µm
Voxel resolution
No
Sample clearing
3D
Full volumetric data
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WHAT IS HREM
3D Microscopy technique built for dense agricultural tissue
High-Resolution Episcopic Microscopy (HREM) captures sequential 2D morphological images as a sample is physically sectioned, which can then be assembled into a precise, perfectly-registered 3D volume. HREM requires no optical clearing, making it ideal for imaging dense, opaque agricultural tissue such as grain, seed pods, and embryos.
Each dataset delivers voxels down to 1 µm, even in larger samples, enabling accurate quantitative morphometry, defect analysis, and phenotypic comparison at scales impossible with conventional imaging.
APPLICATIONS
What can you image with HREM in agriculture?
From plant morphology to embryological studies, HREM handles the sample types that defeat other 3D imaging methods.
🌾
Barley & Cereal Grain Morphology
Resolve the full internal architecture of barley grains in 3D for phenotyping, quality screening, and the study of genetic or environmental effects on development.
🐣
Chicken Embryo Development
Observe the intricate stages of chicken embryo development in 3D monitor organ growth patterns, detect morphological abnormalities, and correlate structural data with genetic or pharmaceutical interventions.
🍋
Citrus Fruit Quality & Defect Analysis
Examine internal citrus structure at micron resolution without destructive sectioning. Identify vascular anomalies, pest damage, disease, and growing-condition effects across whole fruit cross-sections.
🐭
Mouse Embryo Phenotyping
Study early mouse embryo development, characterise the impact of genetic mutations, and analyse environmental factor responses with complete 3D datasets that reveal structural phenotypes invisible in 2D.
🌱
Plant & Root Development
Image developing root tips, floral organs, and tissue in 3D. Track structural change across developmental stages or experimental conditions with precisely registered volume datasets.
🔬
Mouse Embryo Phenotyping
Image whole insects and invertebrates for agricultural pest research, pollinator anatomy studies, and taxonomic morphometry at resolution sufficient for fine appendage and internal organ detail.
Not listed? HREM images most Any dense biological samples
If your agricultural sample is opaque, dense, or too large for confocal imaging, HREM is very likely the right tool. We work with researchers worldwide to image novel sample types. Get in touch and we will advise whether HREM is suitable for your material.
KEY ADVANTAGES
Why researchers choose HREM for agricultural imaging
No Sample Clearing Required
Dense agricultural tissue including grain, seed pods, fruit notoriously difficult to clear optically. HREM images the block face directly, bypassing clearing entirely and preserving tissue integrity.
Whole-Sample Imaging
Image entire agricultural samples, not just thin windows, giving you full-volume morphometric data rather than a representative sub-section.
Micron-Scale 3D Resolution
Achieve voxel sizes down to 1 µm in larger samples, sufficient to resolve vessels, tissue layers, and sub micron features throughout a complete 3D volume.
Quantitative Morphometry
Perform accurate 3D measurement: volume, surface area, length, branching angle. Suitable for statistical phenotyping across large sample sets.
Perfectly Registered Stacks
Because images are captured sequentially from a fixed block face, each frame is inherently aligned, eliminating the registration errors.
Publication-Quality Output
Datasets integrate with Fiji/ImageJ, Imaris, Dragonfly and produce the high-contrast 3D renders expected by top-tier journals.
Common questions about HREM for agricultural research
Can HREM image whole seeds and grain?
Yes. HREM is well suited to imaging whole seeds and grain because it does not rely on optical transparency. Samples are embedded in resin and physically sectioned, so opaque, starchy, or fibrous tissue presents no imaging challenge. Barley, wheat, maize, and rice grain have all been successfully imaged.
What resolution can I expect for plant samples?
For typical agricultural samples, voxel sizes range from 1 µm to around 5 µm depending on sample size. Larger whole-plant sections may be imaged at lower resolution to capture the full volume. Smaller structures such as individual seeds or embryos can be imaged at the highest resolutions.
Can HREM image whole seeds and grain?
Yes. HREM is well suited to imaging whole seeds and grain because it does not rely on optical transparency. Samples are embedded in resin and physically sectioned, so opaque, starchy, or fibrous tissue presents no imaging challenge. Barley, wheat, maize, and rice grain have all been successfully imaged.
What software is used to analyse HREM agricultural data?
HREM datasets are standard TIFF image stacks compatible with Fiji/ImageJ, Imaris, Dragonfly, and AMIRA. Indigo Scientific also offers proprietary tools including a 3D Viewer, Stack Editor, and Stitching Tool. Custom software solutions for specific analysis workflows can be developed on request.
HREM Agricultural sample images
3D reconstructions of plant, grain, and embryological samples captured with HREM.
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