The Microscopy Shared Resource (MSR) is a new, 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.

MSR Imaging Services and Instruments

The MSR has 6 advanced Nikon microscopes with Nikon NIS Elements image acquisition and analysis software, allowing for continuity between instruments and a shared hardware and software experience for all users.

The following are services offered at the MSR:

⦁    Nikon AX R Laser-Scanning Confocal System
⦁    Nikon Crest Spinning-Disk Confocal System
⦁    Nikon SoRa Spinning-Disk Confocal System
⦁    Nikon STORM Super Resolution System* 
⦁    Nikon AX R Multiphoton System*

*Due to the advanced nature of this imaging method, this instrument is generally assisted-use only. However, training is available for advanced users that plan to regularly use this instrument.

For training on any of these instruments, please contact the MSR Manager, Marco Padilla (marco@arizona.edu). 

⦁    Imaging Consultation/Experimental Design: Initial meeting (~30min) with all potential users and MSR staff to discuss imaging and experimental needs. From this meeting, users will be recommended the appropriate microscope and schedule training for the appropriate microscope.

⦁    Microscope Training: Instrument training is generally 2 – 4hrs, split into 2 training sessions. Training #1 focuses on the basics in operating the microscope with an MSR-provided sample and Training #2 focuses on building an imaging workflow based on user needs using a user-provided sample. Required training time is adjusted based on the user’s familiarity with the imaging technique and Nikon hardware and software. Users can be trained on multiple MSR instruments.

⦁    Slide Scanning Service: MSR will perform brightfield and fluorescent imaging on user provided samples using the Nikon BioPipeline High-Content System.

⦁    Assisted STORM Imaging Service: MSR staff provides assisted STORM imaging for users with no prior experience.

⦁    Assisted Multiphoton Imaging Service


  • Image Analysis Training: MSR staff trains users on how to use image analysis platforms to build their own analysis pipeline. Recommended for users that are inclined to learn how to build image analysis tools for current and future projects. Currently, MSR is training users in ImageJ/Fiji, QuPath, and Nikon NIS Elements software platforms.


  • Image Analysis Development: MSR staff develops an image analysis script for users to perform semi- to fully automated image analysis. MSR staff meets with users to design a custom analysis script based on their quantification needs. Recommended for users that need assistance developing an analysis tool but will carry out the analysis for their project. Currently, the MSR develops analysis scripts for users in QuPath and Nikon NIS Elements using General Analysis 3 (GA3).


  • Image Analysis Full Service: MSR staff performs all steps of the quantification process - analysis development, image analysis on user-provided dataset, data export, and manuscript methods for analysis. Depending on the complexity of the analysis, script development will be performed in either QuPath or Nikon NIS Elements.

The following instruments are available at the MSR:
“SoRa” Spinning-Disk Confocal System


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)


Learn More- Nikon SoRa Spinning-Disk Confocal Microscope

Learn More-Info Sheet

“AX R” Laser-Scanning Confocal System


 Nikon AX R Confocal Microscope: 

The Nikon “AX R” system 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 high-speed Resonant scanner with up to 2K X 2K resolution, making this instrument capable of both high-resolution and high-speed imaging. The AX R offers 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.

Featured Capabilities:

  • Confocal imaging with high-speed Resonant scanner
  • Live cell imaging (humidity, temperature, and CO2 regulation)
  • Advanced multichannel imaging (up to 7 fluorophores per sample)
  • Long-working distance 20x objective with 2.3mm working distance
  • Water-immersion 40x objective with automated water dispenser for multi-well imaging

Learn More- Nikon AX R Confocal Microscope

“Storm” Super Resolution System



Nikon N-STORM Super Resolution Microscope: 

The Nikon “Storm” system is our super resolution microscope, capable of achieving 20nm XY and 50nm Z resolution (10x increase in
resolution than a wide field 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)

“AX R MP” Multiphoton System

Nikon AX R Multiphoton Microscope (coming soon):

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

“BioPipeline” Slide Scanner

biopipe test


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.

Featured Capabilities:

  • Optics for polarized microscopy
  • High content imaging with automated slide loader
  • Supports a wide range of fluorophores (DAPI, CFP, GFP, YFP, Cy3, Cy5, and Cy7)
  • Color and fluorescence cameras