Frequently asked questions

Alpenglow Biosciences develops 3D tissue imaging instruments, software, and quantitative analysis platforms. Its technologies include the 3Di™ microscope, 3Dm™ data management, 3Dai™ analysis, and Summit AI™ multimodal analysis. Alpenglow also provides tissue imaging and analysis services for research and translational studies.

Light-sheet microscopy illuminates a thin optical plane of a specimen while detecting fluorescence from that plane. Images acquired at successive depths form a three-dimensional dataset. Selective illumination enables efficient volumetric imaging while reducing light exposure outside the region being acquired.

Hybrid Open-Top Light-Sheet (HOTLS) microscopy combines an open-top sample configuration with illumination and detection optics designed for multiscale 3D imaging. Alpenglow’s 3Di™ HOTLS microscope images optically cleared, intact tissues, from whole-sample surveys to high-resolution regions of interest.

Conventional histology examines thin tissue sections, whereas 3D imaging captures spatial information across tissue depth. Volumetric data lets researchers follow connected structures, measure cell distributions, and examine relationships in three dimensions. The techniques are complementary, with different strengths for morphology, interpretation, and quantitative analysis.

The 3Di™ Hybrid Open-Top Light-Sheet microscope combines high-resolution 3D imaging with the capacity to image large, thick, intact specimens, including tissue volumes up to 1 cm deep. Its Scout path rapidly surveys the sample, while the Zoom path provides fine detail at approximately 0.17 µm/pixel in selected regions, maintaining the context of the larger tissue volume. The open-top design enables accessible sample loading, adaptable holders, and multi-specimen workflows. The microscope also connects to 3Dm™ software for large-volume data processing and downstream quantitative analysis.

The 3Di™ has two imaging paths: Scout at approximately 2 µm/pixel for rapid whole-sample overview and Zoom at approximately 0.17 µm/pixel for high-resolution imaging of selected regions. These numbers describe pixel sampling, not the full optical resolution of the system. See the 3Di technical specifications for the optical configuration.

The 3Di™ supports imaging volumes up to 12 × 7.5 × 1 cm (X × Y × Z), from organoids and biopsies to larger tissue blocks and organs. The standard four-laser configuration uses 405, 488, 561, and 638 nm. An expanded five-laser configuration adds near-infrared excitation at 735 or 780 nm, depending on configuration. Supercontinuum-based tunable excitation for multiplex imaging with up to 12 colors is part of the platform roadmap; confirm availability and configuration with Alpenglow. See the 3Di specifications and fluorescence table.

Alpenglow images a broad range of tissues, including skin and scalp, tumors, brain and nervous tissue, lung, liver, heart, gastrointestinal and lymphoid tissues, placenta, and organoids. Specimens can include thick sections, biopsies, and larger intact samples. Preparation, labeling, specimen geometry, and the biological question determine the recommended workflow.

Yes. Alpenglow works with fresh, frozen, formalin-fixed, PFA-fixed, and formalin-fixed paraffin-embedded (FFPE) tissue. FFPE processing includes deparaffinization and, when appropriate, antigen retrieval prior to staining and clearing. The team can advise on handling and sample preparation for the intended imaging and analysis workflow.

Alpenglow primarily uses workflows adapted from DISCO/iDISCO tissue clearing, including ethyl cinnamate for refractive-index matching. Clearing and staining conditions can be adapted to the specimen, biomarkers, and imaging objectives.

Yes. Alpenglow’s clearing workflows are designed to preserve overall tissue architecture and spatial organization, enabling 3D imaging of continuous biological structures. Small changes in tissue dimensions, including limited shrinkage, can occur during processing. Such changes can be accounted for when quantitative morphometric measurements are required.

No. Alpenglow’s tissue clearing and imaging workflow is non-destructive in the sense that it acquires 3D information without physically sectioning the entire specimen. Tissue architecture remains available for subsequent investigation. Alpenglow has also tested downstream applications involving conventional 2D histology, immunohistochemistry, and spatial biology workflows on previously imaged specimens. Compatibility with a specific downstream assay should be established when planning the project.

Compatible labeling approaches include fluorescent antibodies, nuclear dyes, and probes targeting immune cells, nerves, vessels, and structural tissue features. Compatibility depends on optical excitation/emission bands, labeling quality, and penetration into the specimen. The experimental marker panel is matched to the instrument configuration and study goals.

Yes. Alpenglow can develop or adapt tissue preparation and fluorescence labeling workflows for specific specimens, biomarker panels, and research objectives. Work may include antibody testing, optimization of tissue penetration, and assessment of imaging quality.

3Dm™ processes large volumetric datasets, including image corrections, registration, and stitching. 3Dai™ supports analysis of 3D images, such as segmentation and spatial quantification. Summit AI™ extends analysis across multiple data modalities, connecting 3D tissue images with digital pathology, spatial biology data, and study metadata. These capabilities serve different stages of the data-to-results workflow.

Summit AI™ supports multimodal workflows using 3D tissue images, digital histology such as H&E and IHC, spatial omics datasets, and related study metadata. It can generate quantitative measurements and link findings to the source images. Supported inputs and analyses depend on the specific study design and data formats.

No. Summit AI™ can work with suitable third-party microscopy, digital pathology, and spatial biology datasets. Researchers can analyze existing data independently or combine them with images generated using Alpenglow’s 3Di™ microscope.

Measurements can include cell and tissue segmentation, cell counts, density, morphology, tissue volume, distances, clustering, and spatial-neighborhood metrics. Depending on available labels and imaging quality, analyses can characterize immune-cell distributions, nerve and vessel structures, tissue architecture, and treatment-associated changes.

Yes. Alpenglow can adapt models and analysis workflows for study-specific structures, markers, and research questions. This can include expert annotation, model refinement, quality control, and validation of quantitative outputs. Summit AI also supports workflows informed by expert feedback.

Yes. Summit AI™ can organize and compare quantitative tissue features across samples, regions, cohorts, and experimental groups when the relevant metadata are available. Applications include investigating tissue architecture, cell populations, and spatial relationships in relation to treatment or other study variables.

Depending on project scope, deliverables can include processed 3D image volumes, visualizations, segmentation results, quantitative tables, and analysis reports. Available file formats, viewers, and delivery arrangements are agreed during project planning. For service options, see Alpenglow’s imaging and analysis offerings.

Alpenglow supports research across dermatology, oncology, immunology, neuroscience, vascular biology, fibrosis, and drug development. Examples include measuring immune–nerve relationships in skin, characterizing immune infiltration in tumors, and studying continuous vascular or neural structures through tissue depth.

Volumetric imaging can quantify tissue-level responses to experimental treatments and reveal cellular and structural patterns across specimens. Potential applications include biomarker research, immune profiling, tissue remodeling, and assessment of treatment-associated changes. The most appropriate readouts depend on the disease model and study objectives.

3D tissue imaging adds volumetric information to measurements and interpretations from conventional sections. It supports navigation through tissue depth, visualization of connected structures, and measurement of spatial features throughout a specimen. Conventional histology remains important in established pathology workflows.

Yes. Alpenglow works with research organizations and clinical collaborators on tissue-based biomarkers, disease mechanisms, and pathology-related research. Sample handling, analytic validation, and regulatory requirements depend on the intended use. Research capabilities do not imply authorization for clinical diagnostic use.

Yes. Alpenglow is advancing 3D digital pathology toward clinical applications. Its collaboration with ZEISS involves development of a light-sheet imaging system and bioinformatics for clinical pathology workflows. Its PathNet partnership is focused on clinical-grade 3D AI cancer diagnostics, initially in prostate and bladder cancer. These initiatives remain subject to the necessary development, validation, and regulatory requirements.

Yes. Alpenglow provides services spanning sample preparation, staining, tissue clearing, 3D imaging, data processing, and quantitative analysis. Projects may cover individual stages or more complete workflows. Explore the 3D imaging services page for details.

Use the contact page to share your specimen type, approximate dimensions, preservation method, target markers, and research question. Alpenglow can then advise on feasibility, preparation, scope, and sample submission arrangements before shipment.

Yes. Request a demonstration of the 3Di™ microscope or Summit AI™ through the contact page. The team can discuss your imaging requirements, relevant datasets, and whether a pilot project using representative samples would be appropriate.

Send a short description of your project through the contact form or email info@alpenglowbiosciences.com. Useful details include tissue type, number of samples, research goals, and required imaging or analysis outputs. The team can then discuss scope and next steps.