Microscopy-related resources for Biomedical researchers

This list represents our best effort to put in one place all the microscopy-related instruments and services available to biomedical researchers at the Tucson campus of the University of Arizona (see last item below for some Phoenix campus resources). This list includes microscopy/imaging cores managed by the Chemistry & Biochemistry Research Support Services, the Department of Pathology, RII Core Facilities, UACC Shared Resources, and the COM-P Core Services.

The most complete list of core facilities (of ALL types) on campus can be found on the RII Core Facilities search webpage. If this RII list is missing anything, please let us know as we have access to that website and can add to the list (or make corrections) as needed! If you still can't find what you need, send an email to researchservices@arizona.edu with your request.

The AZ Cores Network list in iLab shows some of the resources at ASU and NAU, in case those might be an option.

Please contact us with suggestions, corrections, questions, or updates!

Updated May 2024

Comparative Pathology Core Lab (Dept. of Pathology, College of Medicine) - provides paraffin and frozen section services including routine and selected special stains. Immunohistochemistry (IHC) using antibody staining protocols on automated platforms. Board-certified pathologist available for experimental advice, quality control, and scoring. Whole slide scanning is available. Located in the College of Medicine building, Room 5207

TACMASR (UA Cancer Center) - Provides paraffin and frozen section services including routine and special stains. Immunohistochemistry (IHC), In Situ Hybridization (ISH) using validated antibody staining protocols on automated platforms. Board-certified pathologist available for experimental advice, quality control, and scoring. In addition TACMASR oversees the UACC's cancer biorepository and has services for organoid generation and culture. Whole slide scanning is provided by the UACC's Microscopy Shared Resource. Located in the University of Arizona Cancer Center, Levy Building, Room 0917

Other related resources:

Vibratome - Used for cutting 200-300um thick sections of fresh or lightly fixed tissue. The RII Imaging Cores - Optical has a vibratome available on a train-to-use basis.
Research grade microwave - Suitable for rapid fixation techniques. The RII Imaging Cores - Optical has a microwave available on a train-to-use basis.

Flow Cytometry Immune Monitoring Shared Resource (UA Cancer Center and UA Research, Innovation & Impact) - ImagestreamX MarkII imaging cytometer - uses flow cytometry technology to acquire microscopic images of fluorescence data from thousands of individual cells in liquid suspension (full or training for self-service).

This Shared Resource also provides full and self-service options for routine flow cytometry. Cell Sorting and multispectral cytometry are available on a full-service basis. Other services include metabolic analysis (Seahorse), routine blood work and immunological analysis (e.g., for clinical trials) and a NanoString GeoMx Digital Spatial Profiler. Located in the University of Arizona Cancer Center, Levy Building, Rooms 0935, 0911, and 0913

Whole microscope slide scanning (fee-for-service)

Nikon Biopipeline Slide - whole slide scanner with brightfield color, polarized light and up to 5 channels of fluorescence. Can scan standard 1x3 as well as 2x3 microscope slides. Maximum magnification is 40x/0.95 dry objective. UACC Microscopy Shared Resource
Olympus VS200 slide scanner - whole slide scanner with brightfield color, and fluorescence filters for DAPI, FITC, TRITC, Cy5, Cy7, CFP, YFP, and mCherry. Maximum magnification is a 60x oil objective. Comparative Pathology Core Lab

Whole microscope slide scanning (do-it-yourself large area scanning)

Most motorized widefield microscopes in core facilities can be used to scan large areas, often in brightfield color, polarized light and multi-channel fluorescence. These are train-to-use instruments that are typically used to scan one slide at a time. Examples include:
- Leica DMI6000
- Zeiss Axio Observer 7 with Apotome III
Most confocal microscopes with motorized stages can be used for high magnification scanning of large areas with the ability to collect focus-stack information as well. In general, confocal microscopes can only scan using fluorescence and are typically used to scan one slide at a time. Examples include:

Leica DMI6000 - 24bit, 5Mpix color camera for brightfield and polarized light images as well as a 16bit, 4Mpix camera and filters for 4 channel fluorescence images. - RII Imaging Cores - Optical

Zeiss Axio Observer 7 with Apotome III - 24bit, 5Mpix color camera for brightfield and polarized light images. 14bit, 5MPix camera and filters for 5 channel fluorescence images in widefield mode with the option to collect confocal-like images (and z-stacks) using the Apotome III in up to 4 channels. Includes Zeiss AI sample finder technology that makes locating and selecting tissue(s) on a slide much easier. - RII Imaging Cores - Optical

Zeiss Axiozoom 16 - Includes a 4Mpix, 16bit camera and filters for DAPI, FITC/GFP, and TRITC with capability for greyscale transmitted light imaging. With a magnification range of 7-112x or 14-224x depending on which front lens is used. - RII Imaging Cores - Optical

Deconvolution captures images using a widefield microscope in a z-stack and then, using a well-established mathematical formula and knowledge of optics, processes the image data to put out-of-focus light back to its estimated point of origin. Often works well at lower light levels than a confocal with image resolution that is equal to, or slightly better than, a confocal microscope.

Deltavision RT (College of Medicine)

Nikon AX-R confocal microscope (UACC Microscopy Shared Resource)

Zeiss LSM880 inverted confocal microscope (RII Imaging Cores - Optical)

Zeiss LSM880 upright multiphoton/confocal microscope with Airyscan (RII Imaging Cores - Optical)

3i Spinning Disk Confocal inverted microscope base with DIC, transmitted light, epi-Fluorescence, spinning disk confocal and Total Internal Reflection (TIRF) capabilities. Includes two fluorescence lasers at 488 nm and 561 nm. The detector is a Photometrics Evolve CCD detector with optional Dual View attachment. Definite Focus is available for maintaining focus during time-lapse experiments. The microscope has a 3i Vector TIRF illumination module with an Andor DU 897 EMCCD for surface specific fluorescence imaging of samples with evanescent wave excitation, penetration depth of ~100 nm in the Z direction. An OKO Lab environmental enclosure is on the microscope for temperature, gas (CO2, O2 and air/N2), and humidity control during experiments. Keck Center for Nano-scale Imaging

Nikon/Crest spinning disk confocal inverted microscope, equipped with a stage-top environmental incubator for live cell imaging and back-illuminated sCMOS Prime95B camera, making it ideal for imaging living samples with minimal phototoxicity. Laser wavelengths: 405, 445, 473, 520, 545, 635nm and fluorescence emission filters: 438/24, 485/20, 511/20, 560/25, 595/31, 685/40. Color camera also available. UACC Microscopy Shared Resource

Nikon Spinning-Disk SoRa - superresolution spinning-disk confocal with a 2x increase in resolution using “SoRa mode”. The SoRa spinning-disk microscope is equipped with an environmental chamber (capable of generating hypoxic conditions) and the high-resolution sCMOS Kinetix camera, making it ideal for super-resolution imaging of live samples (cells, organoids, etc.) with minimal phototoxicity. UACC Microscopy Shared Resource

Perkin-Elmer Operetta CLS (High Content Analysis System‎) designed for fully-automated high-capacity, quantitative cellular analysis of fixed or live cells. Includes a spinning disk system and water immersion objectives up to 63x/1.15. The instrument's data analysis software lets you find even subtle phenotypic changes. RII Functional Genomics Core

LaVision multiphoton (Translational BioImaging Resource)

Nikon AX R Multiphoton Microscope (UACC Microscopy Shared Resource)

Zeiss LSM880 NLO upright multiphoton/confocal with Airyscan (RII Imaging Cores - Optical)

While just about any core facility microscope with the ability to capture digital images could be used for time-lapse, the following microscopes have either stage-top incubators or full environmental enclosures for temperature, gas/humidity control.

3i Spinning Disk Confocal (CBC Keck Center for Nano-scale Imaging)

Deltavision RT (College of Medicine)

Nikon AX-R confocal microscope (UACC Microscopy Shared Resource)

Nikon/Crest Spinning Disk confocal (UACC Microscopy Shared Resource)

Zeiss LSM880 inverted spectral confocal (RII Imaging Cores - Optical)

The Operetta CLS high-content analysis system is designed for fully-automated high-capacity, quantitative cellular analysis of fixed or live cells. It contains the highly sensitive sCMOS camera that provides a large field of view and high resolution image capture (widefield or spinning disk confocal). The Operetta's Harmony software lets you find even subtle phenotypic changes. (RII Functional Genomics Core)

In general, plate readers tend to read the intensity of entire wells, rather than image the individual cells found in the wells (see high-content screening). We are aware that there are a variety of other plate readers on campus, but very few of them are available in core facilities. Sorry, but no one seems to have a complete list...

Functional Genomics Core (RII)

Flow Cytometry Immune Monitoring Shared Resource

10X Genomics Visium spatial gene expression (AZ Genetics Core)

NanoString GeoMx Digital Spatial Profiler is a spatial biology instrument that enables morphology-driven, high-plex profiling on a single FFPE (formalin-fixed paraffin embedded) or fresh frozen tissue section. DSP technology combines standard immunofluorescence techniques with nCounter optical barcoding quantification. This technology allows for spatially resolved, high-plex (10s -10,000s) digital quantitation of proteins or mRNA while maintaining integral information about tissue architecture and spatial relationships between cellular networks. (UACC/RII Flow Cytometry Immune Monitoring Shared Resource)

Nanostring CosMX SMI provides single cell spatial multiomics with formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissue samples at cellular and subcellular resolution. CosMx SMI enables rapid quantification and visualization of up to 6,000+ RNA and 64 validated protein analytes. (UACC/RII Flow Cytometry Immune Monitoring Shared Resource)

3i Spinning Disk confocal with TIRF (CBC Keck Center for Nano-scale Imaging)
Nikon N-STORM (UACC Microscopy Shared Resource)
Nikon Spinning-Disk "SoRa" (UACC Microscopy Shared Resource)
Zeiss LSM880 confocal/multiphoton with Airyscan (RII Imaging Cores - Optical)
Zeiss Elyra S.1 structured illumination microscope (RII Imaging Cores - Optical)

The Keck Center for Nano-Scale Imaging has two atomic force microscopes. An Asylum Cypher S/ES Atomic Force Microscope and a Park NX20 AFM.

RII Imaging Cores - Electron is a full-service Transmission Electron Microscopy (TEM) core facility for bio-medical researchers. Users drop off fixed samples and the core will process the samples for TEM, section the blocks, and provide the user with digital images taken at various magnifications. Sample prep assistance with SEM samples is offered, with imaging offered on the FEI Inspect S SEM in the Keck Center for Nano-scale Imaging on main campus.

Renishaw Reflex RAMAN microscope (Kuiper-Arizona Laboratory for Astromaterials Analysis)

The Translational Bioimaging Resource serves as a university-wide resource for pre-clinical biomedical imaging. The resource has the capability to image small biological constructs, small and large animals, and humans. For imaging small biological constructs and small animals the TBIR includes intra-vital microscopy, MRI, ultrasound, CT, PET, SPECT, and bioluminescence. For imaging larger animals and humans the resource includes MRI and ultrasound. The resource includes personnel to help you with project development and to help you use the equipment.

Definiens Tissue Studio workstation - Translational BioImaging Resource
Image Analysis workstation (Adobe, ImageJ/FIJI, CellProfiler, QuPath, HCImage) - RII Imaging Cores - Optical (LSN)
Nikon Elements workstation - UACC Microscopy Shared Resource
Zeiss ZEN LSM880 post-processing workstation - RII Imaging Cores - Optical (Marley)
Zeiss ZEN SIM post-processing workstation - RII Imaging Cores - Optical (LSN)

OMERO for data management of digital images and/or proprietary microscopy file formats - OMERO is intended to help research labs comply with funding agencies' data management requirements. If your research is human subjects related, OMERO is only suitable for de-identified data (please note: there are ways to securely connect de-identified data with clinical information). Affiliated with the UA Soteria project for securely working with human subjects data in a HIPPA-compliant manner.

Other UA-related resources:

XNAT for data management of digital images in the DICOM format (typically medical imaging instruments)
CYVERSE
UA High Performance Computing (HPC) - Research Desktop Attached Storage Array (R-DAS)
Cloud storage - BOX or BOX Health
Cloud Storage - Google Drive
Cloud Storage - Microsoft Sharepoint/OneDrive (employees only)