Infrastructure & Services

Services

CCIC supports cancer researchers from project design through imaging and quantitative analysis. Use the matrix below to identify which service best matches your sample type, biological question, and expected output.

Service	Best for	Sample types	Typical output	User provides
Cleared tissue light-sheet imaging	Whole-organ or whole-tissue 3D mapping	Mouse organs, tumors, clinical specimens, and other cleared tissues	3D image volumes, stitched datasets, and segmentation-ready files	Fixed labeled tissue, or tissue for coordinated preparation
Expansion microscopy	Nanoscale molecular organization in tissue context	Cells, tissue sections, and compatible FFPE or fixed samples	Expanded 3D image volumes and subcellular feature maps	Fixed samples and markers of interest
Thick-section cyclic immunofluorescence	Tumor microenvironment profiling beyond thin sections	30–50 micron FFPE or fresh-frozen sections	Multiplexed 3D antibody panels and marker maps	Tissue sections, marker priorities, and biological question
Live spheroid imaging	Drug response, invasion, and dynamic cell behavior	Spheroids or organoids in matrix or multi-well formats	Time-lapse 3D imaging and response metrics	Culture model, perturbation design, and timeline
Image analysis and visualization	Segmentation, quantification, registration, and interpretation	CCIC-generated or compatible imaging datasets	Quantitative tables, visualizations, annotations, and analysis consultation	Imaging data, analysis goals, and preferred outputs

Sample Preparation Guidance

Successful 3D and multiplexed imaging depends on matching tissue handling, labeling, clearing, expansion, and acquisition strategy to the biological question. CCIC can help users plan sample preparation during project consultation.

Supported sample classes

Mouse organs and other mouse tissues, including cleared specimens for large-volume imaging.
Human and mouse tumors, clinical specimens, and compatible FFPE material.
Thick tissue sections for cyclic immunofluorescence and 3D tissue context.
Cleared specimens, expanded tissues, and fixed samples for high-resolution imaging.
Spheroids, organoids, and 3D cultures for live or fixed volumetric imaging workflows.

Before intake

What tissue type, species, disease model, or culture system will be imaged?
Is the specimen live, fixed, FFPE, frozen, cleared, expanded, or still being prepared?
What imaging depth, field of view, resolution, and number of markers are needed?
Are antibody labeling, endogenous fluorescence, clearing, expansion, or live-imaging conditions required?
Will the project need segmentation, registration, visualization, quantitative measurements, or other analysis needs?

Compatibility depends on tissue type, fixation, labeling strategy, assay format, and downstream analysis goals. CCIC staff can help determine the most appropriate preparation path after intake through iLab.

Data and Analysis Deliverables

CCIC projects may include imaging data, metadata, visualization, and quantitative analysis outputs matched to the selected service and project scope.

Raw and processed 3D image volumes from light-sheet, oblique-plane, expansion, or thick-section imaging.
Stitched, registered, or visualization-ready datasets for large or multiscale specimens.
Segmentation masks, labeled objects, region annotations, and measurement tables when analysis is included.
Object-level measurements such as volume, intensity, morphology, spatial position, and proximity relationships.
Representative renderings, annotated views, exported tables, and analysis consultation for figures or follow-up experiments.
BioHPC-backed data handling and analysis support for large imaging datasets, when appropriate for the project.

Final deliverables are defined during consultation and depend on sample readiness, acquisition plan, data size, analysis needs, and available workflows.

Infrastructure

Multiscale Cleared Tissue Axially Swept Light-Sheet Microscope

A custom 4-axis microscope that offers both macroscale and nanoscale imaging of chemically cleared tissues.
The macroscale module provides a lateral and axial resolution of 2.5- and 4.2-microns, respectively, over fields of view from 2.1 mm to 21 mm, ideal for large specimens.
The nanoscale module offers 330 nm resolution across a 340x340 micron field of view.
Fully automated microscope operation and switching between imaging modes – identify biological features of interest with the macroscale module and seamlessly switch to dive deeper with the nanoscale module.
Key upgrades: Addition of a 405 nm laser, enabling operation of the microscope in a cyclic multiplexed format.

Upright Cleared Tissue Axially Swept Light-Sheet Microscope

Position samples laterally on large travel range stages to interrogate from the top. Particularly useful to analyze cm-sized clinical specimens and facilitates the handling of expanded specimens.
Equipped with an epi-fluorescence module for quick identification of regions of interest.
Resolution of 440 and 330 nm in aqueous and high refractive index media, respectively. Suitable for high-resolution studies of cellular and subcellular features. For expanded tissues, the resolution improves linearly with the expansion coefficient, achieving 22 nm, with molecular specificity, in tissue contexts.

Cleared Tissue Axially Swept Light-Sheet Microscope – Variant 1

This microscope provides ~700 nm resolution over a 1 mm by 1 mm field of view, ideal for imaging centimeter-sized samples.
Key upgrades: Addition of a numerical aperture 1.15 multi-immersion objective specifically designed for cleared tissue imaging. Increases the photon collection 6-fold and provides ~215 nm lateral resolution.
New image acquisition computer to enable faster, more efficient data collection.

Cleared Tissue Axially Swept Light-Sheet Microscope – Variant 2

~330 nm isotropic resolution over a 340x340 micron field of view, enabling evaluation of sub-cellular architectures with unparalleled precision.
Key upgrades: Addition of a back-thinned, high quantum efficiency scientific CMOS camera to enable the detection of low-abundance molecular features, ensuring the capture of detailed structures implicated in cancer cell regulation.

Benchtop MesoSPIM

~2-micron isotropic resolution across a 2.6 mm field of view, enabling rapid imaging of large areas.
Accompanied by a Mecademic Meca500 industrial robot for automated sample loading and features a custom-designed 24-sample rotary carousel, which can be expanded to accommodate upwards of 60 samples for high-throughput characterization of tissues, metastatic colonization with single cell sensitivity, and other large-scale biological processes.

High-Resolution Oblique Plane Microscope

Optimized for imaging aqueous specimens, such as spheroids and sectioned tissues with ~400 nm lateral and ~580 nm axial resolution.
Captures of volumetric images at speeds of up to 800 planes per second, making it ideal for high-throughput and cyclic immunofluorescence imaging applications.
Equipped with a water-dipping objective enabling the study of complex 3D cellular structures in their native environments.
The single-objective design ensures sample sterility, a critical requirement for live-cell imaging and longitudinal studies, while also supporting multi-well plate formats, rendering the system a powerful tool for targeted pharmacological and genetic screens, and for generating high-resolution insights into cell-cell interactions, drug responses, and dynamic changes within tumor microenvironments.
Key upgrades: Addition of a laser launch for increased spectral multiplexing during cyclic immunofluorescence workflows. Integration of a fluidic exchange system to automate antibody delivery and sample washing, which will significantly increase efficiency, reproducibility, and throughput for large-scale imaging experiments.