A volunteer and collaborative effort to bring information about shared microscopy facilities to the University of Arizona and the community.

Nikon AX R Multiphoton Microscope

Nikon AX R Multiphoton Microscope

Coming in the late fall of 2023.

The Nikon “AX R MP” microscope is an upright multiphoton system ideal for intravital imaging and thick samples. This instrument is equipped with dual IR lasers (1 tunable and 1 fixed) for fast multichannel imaging, the same highspeed Resonant scanner in our AX R system, and a 22mm field of view, allowing more data to be collected in a single image. The AX R MP is optimized to image green (i.e. AF488), red (i.e. AF568), and far-red (i.e. AF647) fluorophores, with the ability to acquire second harmonics generation for label-free imaging. This system has a wide selection of objective lenses for multiphoton imaging, including two glycerin-immersion objectives (10x 0.5NA and 20x 1.0NA) and a water immersion 20x 1.0NA objective lens, and is configured with a large-clearance “gate-stand” to provide space for intravital imaging setups (800mm W X 400mm H X 730mm D). Due to the nature of this advanced technique, the AX R MP system is assisted-use only and the MSR provides a bench area for setup and ancillary equipment.

Featured Capabilities:

  • High-speed imaging with Resonant scanner
  • Tunable IR laser range: 680nm – 1300nm
  • Dual IF lasers (1 tunable and 1 fixed) for fast multichannel MP imaging
  • Second harmonics generation for label-free imaging
  • Upright microscope with a large clearance stand to accommodate intravital imaging stands

Nikon Spinning-Disk SoRa - superresolution

Nikon CSU-W1 Spinning-Disk Super Resolution by Optical Pixel Reassignment (SoRa)

The Nikon “SoRa” system is our most advanced spinning-disk confocal and merges the advantages of confocal imaging with a 2x increase in resolution using “SoRa mode”, making this both a confocal and super resolution microscope. 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.

Featured Capabilities:

  • Confocal imaging (Yokogawa CSU-W1 Optics)
  • Live cell imaging (humidity, temperature, and CO2 regulation)
  • Super resolution (2x resolution using SoRa mode)

Nikon AX R Confocal Microscope

Nikon AX R Confocal Microscope

The Nikon AX R is an inverted laser-scanning confocal microscope and is our most capable instrument. The AX R has both a traditional, high resolution Galvano scanner and a highspeed Resonant scanner with up to 2K X 2K resolution, making this instrument capable of both high resolution and the largest selection of laser lines (405/445/488/568/594/640/730), allowing the microscope to excite up to 7 fluorophores with clear spectral separation. This instrument has the widest range of objectives lenses, including a long working distance 20x 0.7NA objective with 2.3mm of working distance and water immersion 40x 1.25NA objective with automated water immersion dispenser, ideal for long-term, live cell and multi-well plate imaging.

  • Confocal imaging with high speed Resonant scanner
  • Live cell imaging (humidity, temperature, and CO)
  • Advanced multichannel imaging (up to 7 fluorophores per sample)
  • Long-working 20x objective with 2.3mm working distance
  • Water-immersion 40x objective with automated water dispenser for multiwell imaging

Microscopy Shared Resource

The Microscopy Shared Resource (MSR) is an advanced microscopy facility located at the UA Cancer Center, servicing the immediate needs and future demands of biomedical and translational researchers.

The MSR provides several advanced instruments and services for all UA researchers, including confocal microscopy, super resolution microscopy, slide scanning, live cell imaging, multiphoton and intravital imaging, advanced image analysis, and much more. In addition to providing advanced instrumentation and imaging services, the core facility is a model of academic collaboration. MSR provides a space for on-site workshops, imaging seminars highlighting cutting-edge imaging approaches, demonstrations of next components/instruments, and support to the broader imaging community by building an “imaging culture” on campus.

UA Cancer Center, rooms 0930 (Levy building), 0960 (Salmon building)

Contact the Shared Resource for acknowledgement text. As an NIH P30 center, it is crucial that users of this Shared Resource acknowledge the support of the Cancer Center Support Grant (P30 CA023074).

Core Staff
Ghassan (Gus) Mouneimne, PhD Director, UACC Microscopy Shared Resource 520-626-4616 gmouneimne@arizona.edu
Marco Padilla-Rodriguez, PhD Manager, UACC Microscopy Shared Resource 520-626-6041 marco@arizona.edu
David Jones Jr Staff, UACC Microscopy Shared Resource djonesjr@arizona.edu
University of Arizona Cancer Center wordmark

This facility is administered by the University of Arizona Cancer Center (NCI P30 CA023074), Tucson, Arizona.

Zeiss Axio Observer 7 with Apotome III Microscope

Zeiss Axio Observer 7 with Apotome III Microscope 

This is a multi-function, motorized inverted microscope that includes a brightfield color camera and a 14bit greyscale fluorescence camera. The addition of the Apotome III attachment allows this microscope to give crisp "confocal-like" z-stack images of thinner samples. Thinner means out to approximately 20um in thickness, making this microscope suitable for samples such as: cells on a coverslip, paraffin and standard cryostat sections.

How does this microscope create "confocal-like" images? - The Apotome III projects a grid structure into the focal plane of the specimen, then moves it into different positions using a scanning mechanism. At each grid position, the Apotome III automatically acquires a digital image. The system processes all images into one optical section with improved contrast and increased resolution using a patented algorithm. The resulting image is free from grid structures. (SOURCE: Zeiss) Deconvolution software is available to further improve the image quality of the Apotome images.


  • AI sample finder - using a unique contrasting method, the microscope can find multiple wells in a plate, unstained sections on a slide, or locate the edges of a coverslip . Very useful for setting things up to scan multiple areas or large area scanning of tissue that's otherwise difficult to see by eye.
  • Colibri 7 LED illuminator allows for 7 specific excitation wavelengths (including a near-IR wavelength). With just two multi-band filter sets, switching between channels is significantly faster than microscopes using filter cubes, making tile scanning in fluorescence much faster. Due to spectral overlap issues, we should be able to capture up to 5 channels in regular widefield fluorescence and 4 channels with the Apotome III (which does not work with near-IR wavelengths). To see how your dyes might work with this system, see our configuration at FPbase.
  • Capable of color brightfield imaging (e.g., histology stained slides), Differential Interference Contrast (DIC, e.g., unstained cells), simple Polarized light imaging (crossed linear polarizers, e.g., Picrosirious red staining), and multiple channels of fluorescence as well as combinations of any of these imaging modes.


  • Objective lenses: 5x/0.16NA dry, 10x/0.45NA dry, 20x/0.8NA dry, 40x/1.3NA oil, 63x/1.4NA oil (a 40x/0.95NA dry objective with coverslip correction is available upon advance request)
  • Colibri 7 excitation wavelengths: UV 385/30nm, V 423/44nm, B 469/38nm, G 555/30nm, Y 590/27nm, R 631/33nm, FR 735/40nm
  • Zeiss 489112-9110-000 (suitable for fluorescent dyes like DAPI, FITC, DsRed, CY5, and CY7) and 489091-9110-000 (suitable for fluorescent dyes like CFP, YFP, and mCherry) multiband filter sets

NOTE: See our news announcement Introducing the Zeiss Axio Observer 7 inverted microscope with Apotome III for a discussion of what types of samples would benefit from this microscope, as well as a list of weaknesses.


Nikon N-STORM Super Resolution Microscope

Nikon N-Storm

The Nikon “Storm” system is our super resolution microscope, capable of achieving 20nm XY and 50nm Z resolution (10x increase in resolution than a widefield fluorescence microscope). STochastic Optical Reconstruction Microscopy (STORM) is our most advanced imaging modality offered at the MSR and requires a consultation with our MSR team prior to experimentation and sample preparation. This instrument is also capable of acquiring 3D STORM images and is currently optimized to image two fluorescence channels (488nm and 647nm).

Due to the nature of this advanced technique, the Storm system is assisted-use only and the MSR will provide optimized protocols and imaging buffers for users.

Featured Capabilities:

  • Super resolution imaging (10x resolution)
  • 3D STORM (with astigmatism lens)
  • Optimized for 2-channel STORM imaging (488nm and 647nm)

Nikon/Crest spinning disk confocal

Nikon/Crest spinning disk confocal

Nikon Crest X-Light V2 Spinning-Disk Confocal

The Nikon “Crest” system is an inverted, spinning-disk confocal microscope that allows for high-throughput, confocal imaging of cell and tissue samples. The Crest Spinning-Disk is ideal for applications that require the increased resolution and contrast of confocal imaging with the speed of a widefield system. The Crest Spinning-Disk is equipped with a stage-top environmental incubator for live cell imaging and backilluminated sCMOS Prime95B camera, making it ideal for imaging living samples (cells, organoids, etc.) with minimal phototoxicity.

  • Objective lenses: Plan Fluor 4x/0.13, 10x/0.3; Plan Apochromat Lambda 20x/0.75, 40x/0.95, 60x/1.4 (oil)
  • Laser wavelengths: 405, 445, 473, 520, 545, 635nm
  • Fluorescence emission filters: 438/24, 485/20, 511/20, 560/25, 595/31, 685/40
  • To examine how your fluorescent labels would work with the lasers and filters, see: https://www.fpbase.org/microscope/NSt3svJtnMmkQL7aC69Hb3/
  • Additional brightfield color camera (Nikon DS-F13) and DIC (20x, 40x, 60x), Phase contrast (4x, 10x) imaging modes
  • Stagetop incubation chamber for long term imaging, with the capability of performing hypoxia studies.
  • CFY/YFP FRET imaging
  • Multiple Nikon software modules for multi-dimensional imaging, object tracking, image analysis, and deconvolution

Nikon BioPipeline SLIDE

Nikon Biopipeline SLide scanner

Nikon BioPipeline Slide - High Content Imaging System

The Nikon “BioPipeline” is an automated, widefield slide scanning system equipped with a Marzhauser Slide Express 2 loader with a 120-slide capacity for high-throughput imaging, optics for polarized microscopy, and optics to support UV – IR imaging. Due to the robotic slide loader, the BioPipeline is ideal for high content projects that require imaging several slides in an automated fashion and supports both 1x3 and 2x3 glass slides. The BioPipeline is an assisted-use only system and is offered as a service at the MSR. MSR staff with work with users to design an imaging workflow and acquire the images based on the user’s needs. Researchers interested in this service, supported slides, and turnaround time can view our Slide Scanning Request Form on iLabs. This whole slide imaging (WSI) device has:

  • 2x/0.1, 4x/0.2, 10x/0.45, 20x/0.75, 40x/0.95 Nikon CFI Plan Apo Lambda dry objectives
  • A color camera (Nikon DS-FI3) for brightfield (transmitted light) imaging of stained microscope slides prepared with routine histology and immunohistochemical stains.
  • Optics for polarized light imaging of stains such as picrosirious red.
  • A 16bit greyscale (Hamamatsu ORCA Flash 4.0 v3) camera for multicolor fluorescence imaging. Emission fIlters for fluorescence dyes such as DAPI, CFP, GFP/FITC, YFP. CY3, mCherry, CY5, and CY7 (note - due to significant spectral overlap, it is highly unlikely that any more than 5 channels could be acquired/slide). To assist you, see: https://www.fpbase.org/microscope/wwUUo5S7igkNu6DpxdLJXE/
  • In addition to the standard 1x3 inch glass microscope slides, this scanner can also image the less common 2x3 inch glass microscope slides.
  • An off-line workstation for image analysis (Nikon software) and a 200TB MS Windows file server were part of this purchase.

DeltaVision RT Deconvolution Microscope

Deltavision microscope

The DeltaVision RT Deconvolution Microscopy System includes a research-grade inverted Olympus IX 70 microscope (with objectives from 4x to 100x, a cooled CCD camera, fiber-optic coupled mercury arc lamp, high-speed filter changers, electronic shutters and a high precision x-y-z positioning system) that is coupled to a computer workstation running Linux and vendor-supplied software called SoftWorX. Automated multiple wavelength (Blue, Green, Red and Far-red) and/or time lapse imaging experiments can be performed on either fixed tissues or cultured cells (Temperature and gas-mix can be controlled). The Microscope is capable of high resolution fluorescence images, 2D and 3D time-lapse, lower light intensity (compared to a confocal laser) means it is friendlier to live cells, has a greater dynamic range (4096 intensity levels) compared to older confocals, up to 4 probes per data set (limited to the available filter sets).

Training: Users must complete a minimum of 3 hours of training time before they will be allowed to use the instrument without assistance.

Fees: Trained users will be charged a fee of $22.00/hour for time on the instrument (microscope use and/or computation are currently the same fee). Training or Asssisted use are $38.00/hour (NOTE: these rates are internal UA only, updated Feb 2021).

Research Microscopy Core Service

Featuring a DeltaVision RT Deconvolution Fluorescence Microscope with full environmental controls.

Core Staff
Chris Pappas, PhD Director, Research Microscopy Core Service (College of Medicine) 520-626-5209 ctpappas@arizona.edu
Cellular & Molecular Medicine

This facility is administered by the Cellular & Molecular Medicine department of the College of Medicine at the University of Arizona.