3D tissue imaging microscope
3Di™ Hybrid Open-Top Light-Sheet Microscope
A dual-path light-sheet microscope combining rapid whole-sample 3D imaging with high-resolution 3D imaging of selected regions.
Meet the instrument
The 3Di™ microscope
A hybrid open-top light-sheet system designed for multiscale imaging of optically cleared biological tissues.
Scout-to-Zoom workflow
Whole tissue context first. High-resolution 3D detail where the biology matters
The 3Di™ microscope combines rapid whole-sample scouting with targeted high-resolution acquisition, allowing researchers to identify regions of interest within intact tissues and examine their 3D architecture in greater detail.
Scout the whole sample
Acquire a rapid 3D overview to visualize tissue organization and identify structures of interest.
Select regions of interest
Navigate the volumetric dataset and select specific regions for higher-resolution imaging.
Zoom into submicrometer detail
Examine selected regions at higher resolution while retaining their location within the broader tissue context.
Whole rat heart overview
Rapid low-resolution imaging provides whole-sample context and navigation.
ROI from the whole rat heart
High-resolution imaging captures local structural detail inside selected tissue regions.
HOTLS architecture
Hybrid open-top optics for multiscale tissue imaging
The 3Di™ microscope combines light-sheet illumination with complementary detection paths to image optically cleared tissues across different spatial scales.
Peer-reviewed optical design
Nature Methods (2022)
The HOTLS architecture was described and experimentally demonstrated in a peer-reviewed study of multiscale cleared-tissue imaging.
Read the publication →
Hybrid Open-Top Light-Sheet optical layout
Schematic showing the illumination and detection geometry of the HOTLS architecture.
Open-top sample flexibility
Designed to accommodate diverse tissue specimens
The open-top design of the 3Di™ microscope provides direct access to the sample and accommodates different specimen shapes, sizes, and holder configurations. From small biopsies and tissue blocks to larger cleared specimens, the system supports flexible sample positioning and imaging workflows.
Open-top access
Practical sample loading and positioning for intact tissue imaging workflows.
Flexible access
Holder configurations
Holder options support diverse specimen formats and experimental needs.
Sample formats3D Cell Models
Organoids, spheroids & engineered tissues
Model Organisms
& Embryos
Small organisms, embryos & plants
Biopsies &
Tissue Specimens
Intact biopsies & surgical specimens
Intact Organs
Organs from model organisms
Large-Format
Tissue Specimens
Thick sections & large tissue blocks
Illustrations represent specimen types imaged using Alpenglow’s 3Di™ microscope. Examples are not exhaustive. The size progression is conceptual, not a calibrated scale.
Easy sample access
The open-top format supports straightforward sample loading, positioning, and handling for cleared tissue imaging.
Flexible holder configurations
Sample holders support different specimen formats, including organoids, biopsies, tissue blocks, and whole organs.
Multi-specimen acquisition
Supports scanning multiple specimens within the same acquisition session.
Large scan area
The microscope’s large scan area, up to 12 cm × 7.5 cm × 1 cm, enables the acquisition of complete 3D images of large biological tissues.
LUMI microscope control software
From scan setup to acquisition, all in one interface
LUMI provides an integrated interface for controlling the 3Di™ microscope, from scan configuration and live visualization to Scout and Zoom acquisition. Researchers can preview their specimens, navigate regions of interest, and manage imaging parameters within a single environment.
LUMI: Integrated microscope control
Scan configuration, live visualization, and Scout-to-Zoom navigation within a single interface.
Streamlined scan setup
Configure acquisition parameters and imaging regions through a unified interface, reducing the need to navigate between separate controls.
Live Scout and Zoom preview
Visualize specimens in real time using Scout and Zoom modes to guide imaging decisions before acquisition.
Region-of-interest navigation
Use the Scout overview to identify and navigate to regions of interest for targeted high-resolution acquisition.
3D imaging gallery
Explore intact tissues in three dimensions
See representative datasets acquired with the 3Di™ microscope, revealing tissue architecture, cellular organization, and structural relationships across a range of biological specimens.
Technical specifications
Explore the technical capabilities of 3Di™
Review the optical configuration, imaging modes, sample compatibility, and fluorescence options of the 3Di™ Hybrid Open-Top Light-Sheet microscope.
Instrument specifications
Optical, imaging, specimen, and acquisition parameters.
| Specification | Value |
|---|---|
| Optical configuration | |
| Microscope architecture | Hybrid Open-Top Light-Sheet (HOTLS) |
| Maximum collection NA | 0.7 |
| Maximum illumination NA | 0.06 |
| Scout magnification | 2.5× |
| Zoom magnification | 40× |
| Imaging modes and sampling | |
| Scout pixel sampling | 2 µm/pixel |
| Zoom pixel sampling | 0.17 µm/pixel |
| Specimen compatibility | |
| Maximum specimen dimensions | Up to 12 × 7.5 × 1 cm (x, y, z) |
| Refractive index range | 1.33–1.56 |
| Multiwell / multi-specimen scanning | Supported |
| Fluorescence and detection | |
| Standard excitation lasers | 405, 488, 561, 638 nm |
| Expanded excitation configuration | Five-laser configuration with additional near-infrared excitation |
| Cameras | 2 × Hamamatsu ORCA Fusion BT |
| Microscope control | |
| Control software | LUMI graphical user interface |
Fluorescence and multiplexing
Excitation options for different fluorescence workflows
Select from standard or expanded laser configurations to accommodate different fluorophore combinations and experimental requirements.
4-laser configuration
Excitation at 405, 488, 561, and 638 nm for established multichannel fluorescence imaging workflows.
5-laser configuration
Additional near-infrared excitation extends fluorophore selection for more complex fluorescence panels.
Toward 12-color multiplex 3D imaging
A supercontinuum-based configuration is planned to provide tunable excitation across a broad spectral range, with the goal of supporting multiplex imaging of up to 12 colors. This capability is under development and is not part of the standard instrument configuration.
High-resolution 3D fluorescence imaging reveals an entire hair follicle in an intact HS biopsy, including individual cells, nerve networks, mast cells, and measurable spatial relationships.
This dataset presents high-resolution 3D fluorescence imaging of a hair follicle within an intact hidradenitis suppurativa (HS) skin biopsy, revealing follicular architecture, surrounding nerve networks, and individual cells throughout the imaged tissue volume.
The visualization begins with a 3D reconstruction of the complete hair follicle, showing its morphology and the intricate distribution of nerve fibers and mast cells in the surrounding tissue. Virtual 2D sectioning enables detailed examination of cellular structures at different depths without physically sectioning or destroying the specimen. The dataset is then visualized again in 3D to reveal the spatial organization of these structures.
Fluorescence markers:
- TO-PRO-3 (blue): Cell nuclei
- PGP9.5 (white): Nerve fibers
- Tryptase (green): Mast cells
The combination of high spatial resolution and volumetric imaging enables quantitative assessment of follicular morphology, cell counts and densities, nerve architecture, and distances between cells and nerve fibers.
This approach supports the investigation of follicular structures and neuroimmune interactions in HS while preserving their spatial relationships within the intact tissue.
Learn more about dermatology applications
Learn more on image analysis using Summit AI(TM)