Cellular Imaging - Services

With decades of experience in microscopy and image analysis, the Cellular Imaging Facility Core Director is available to support the research of SWEHSC members and their labs. The Director can help you plan out an experiment from the very beginning, to come alongside to train and support your lab staff as they use key pieces of instrumentation, to assist with data analysis, as well as suggest appropriate image manipulations and text for your manuscripts or grant applications.

The Director is available to schedule a meeting to discuss your concerns, or is willing to come to SWEHSC member labs for more informal consultation or support. Please contact us.

It is important that SWEHSC members remember to acknowledge the SWEHSC Center Grant (P30 ES006694) when publishing manuscripts or abstracts that utilized the services of the SWEHSC facility cores and resource. UA Cores affiliated with Cellular Imaging include: UACC TACMASR (histology, IHC), UACC Microscopy Shared Resource (slide scanning, microscopy, image analysis), UACC/RII Flow Cytometry & Human Immune Monitoring Shared Resource, RII Imaging Cores (Electron - biological TEM; Optical - confocal, multiphoton, superresolution, widefield), and Image Analysis (Imaging Cores - Optical, UACC MSR), and the RII Translational BioImaging Resource (small animal imaging by MRI, microCT, ultrasound, fluorescence/bioluminescence).

• Color brightfield light microscope – Leica DMI6000 with Leica DFC450 color CCD camera, Zeiss Axio Observer 7 with Apotome III
• Color brightfield whole microscope slide scanner – The Leica DMI6000 and Zeiss Axio Observer 7 with Apotome III can stitch together multiple images over large areas. The UACC's TACMASR has a Nikon BioPipeline Slide microscope slide scanner (color brightfield, polarized light, up to 5 channel fluorescence). The Department of Pathology Core Service lab will have an Olympus VS200 slide scanner for color brightfield and 4 channel fluorescence. 
• Fluorescent stereo microscope – Zeiss Axiozoom 16 with Hamamatsu Flash 4.0 sCMOS camera
• Fluorescence widefield microscope (4-5 colors) - Leica DMI6000 with Hamamatsu Flash 4.0 sCMOS camera, Zeiss Axio Observer 7 with Apotome III, see also the whole microscope slide scanner.
• Confocal microscope(s) – RII Zeiss LSM880, RII Zeiss LSM880MP, CBC 3I spinning disk confocal, UACC Nikon spinning disk confocal, UACC MSR Nikon AX-R confocal (Note: the  Zeiss Axio Observer 7 with Apotome III can give confocal-like images for thin samples up to about 20um)
• Multiphoton/confocal microscopy - RII Zeiss LSM880MP, RII/TBIR Intravital confocal/multiphoton, UACC MSR Nikon AX-R multiphoton (coming late fall 2023)
• Superresolution fluorescence – RII Zeiss Elyra S.1, RII Zeiss LSM880MP with Fast Airyscan, UACC MSR Nikon N-STORM microscope.
• Flow Cytometry/Cell Sorter (see the UACC/RII core's iLab page) - FACSCanto II, LSR II, FACSAria III, Cytek Aurora, Imagestream II (imaging cytometer), Cytek Aurora 5 Laser Spectral Flow Cytometer
• Electron microscopes - RII FEI Tecnai Spirit TEM, for biological Scanning EM, see the CBC FEI Inspec-S SEM (Note: there are a number of campus TEMs and SEMs that are restricted to non-biological samples)
• Small Animal Imaging - MRI (small animal & clinical), High Resolution Ultrasound, MicroCT, Bioluminescence/Fluorescence Small Animal Imaging, PET & SPECT imaging
• Atomic Force Microscopes (AFM) – several in the UA Chemistry & Biochemistry's Keck facility
• Image analysis software - SWEHSC Cellular Imaging - HCImage (Hamamatsu) workstation; MSR - Nikon image analysis software tools, Quantitative Digital Histology
• Data management resources - University of Arizona Library Data Cooperative (data management plans, ReDATA repository, data Science & visualization), University of Arizona's OMERO instance (for the management & curation of digital image data from microscopes and other sources), University of Arizona's XNAT (for the management of image data, primarily medical imaging data in the DICOM format - XNAT software home page), University of Arizona's SOTERIA (a secure environment for working with HIPPA/PII clinical data)

If you can't find what you need in this list, contact us and we will help you look for what you need. There are additional microscopy and imaging resources at the other state universities, which can be located in the AZ Cores Network. 

There are a number of reasons to use a full-service facility.

• Full-service labs allow investigators to "pay as you go".
• Service labs typically use newer equipment that receives regular maintenance.
• The staff in the facilities often have decades worth of experience.
• If you are trying something new, a full service lab can walk you through the entire process.

Paraffin/Frozen Section Histology & Immunohistochemistry (IHC)

TACMASR (University of Arizona Cancer Center) - Users bring fixed or snap-frozen tissues to the Lab and in a week to 10 days they should expect to have microscope slides. Slides can be stained with routine and special stains, or left un-stained so that users can perform immunohistochemistry (IHC) or immunofluorescence (IF) on their samples. Users can have TACMASR perform computer-controlled IHC or in situ hybridization (ISH) on their samples using one of TACMASR's previously verified antibodies. Advice and microscopic analysis by a board certified Pathologist is available.

Whole Slide Imaging (WSI)

Microscopy Shared Resource (University of Arizona Cancer Center) - users will drop off slides for scanning with instructions regarding the magnification required (2x, 4x, 10x, 20x, 40x) and the imaging mode required (color transmitted light, color polarized light, up to 5 channel fluorescence). After the scanning is completed users will be given access to a digital file that represents the scanned area. Image analysis routines can be developed in the Nikon software if required.

Electron Microscopy (EM)

Imaging Cores - Electron (RII Core Facilities) - This facility specializes in biological transmission EM. Users bring fixed samples and can expect either 1um plastic sections, TEM grids, or TEM digital photos, depending on their research needs. The Keck Imaging facility in Chemistry can perform scanning EM of biological samples.

Flow Cytometry & Immune Monitoring

Flow Cytometry & Immune Monitoring Shared Resource (RII Core Facilities & University of Arizona Cancer Center) - This facility provides full-service flow cytometry and cell sorting capabilities. Their workhorse instrument, a BD FACSAria III, can count 11 different characteristics simultaneously, is BSL2 compliant, and can sort into 4 different sub-populations. Additional information is available at the UACC's website.

The Facility Core provides a number of one-on-one training opportunities for SWEHSC faculty, staff, students and post-docs. These can be formal training opportunities related to a specific instrument/technique, or informal explanations tailored to a specific research question.

Instruments

Mr. Cromey has specific expertise in light, confocal, superresolution, and electron microscopy, as well as image analysis and time-lapse imaging of live cells. He can provide the following types of instrument-specific training:

• YouTube videos on Sample Preparation for microscopy 
• Laboratory light microscopes - There are a number of very nice light microscopes in research labs that are often poorly used, dirty, and mis-aligned. Mr. Cromey can teach your lab staff how to care for, and align, your lab microscope so that it is used properly and will last for a long time. No cost for the laboratories of SWEHSC investigators.
• UACC Spinning disk confocal (Nikon) - Mr. Cromey previously managed this instrument and can provide hands-on support for SWEHSC users. 
• RII Zeiss LSM880 confocal microscopes - Mr. Cromey can provide hands-on support and training for SWEHSC users on these microscopes.
• Light Microscopes and Image analysis workstations - Learn how to use these instruments to acquire images for a specific research purpose or for performing an image analysis experiment. The Leica DMI6000 and the Zeiss Axio Observer 7 with Apotome III have an hourly usage fee, but the image analysis workstation is freely available. There is no cost to SWEHSC investigators for any additional off-microscope consultation.
• Electron microscopy - while Mr. Cromey does not provide instrument training for the TEM, he does have 15 years of electron microcopy experience that users can tap into when preparing and interpreting their experiments. 
• Superresolution Structured Illumination Microscope (SR-SIM) - Mr. Cromey manages this instrument and provides all the training and technical support. New users learn about the optics and mathematics behind this technique. 
• Other instrument training (not specifically provided by the Cellular Imaging Resource) - Interested users can contact the other facilities (Flow Cytometry, TACMASR) associated with the Resource to receive training directly from the staff in those facilities. There are fees associated with the training and/or equipment use, follow the web links to learn more details.

Please note: since RII pays a portion of Mr. Cromey's salary, there is a personnel/training charge when using the RII cores, along with the standard hourly usage fees. Using the SWEHSC subsidy account (applies to RII cores only) for such charges reduces the cost for the investigator.

Digital Imaging

• Introduction to Scientific Digital Imaging - A four hour workshop that has traditionally been given annually. We are currently in the process of transitioning this workshop to an on-line learning platform so that it can be available year-round.
• Digital imaging software - Learn how to correctly use Adobe Photoshop to process digital images and set up figures for publications. No cost for the laboratories of SWEHSC investigators.
• Digital imaging ethics - Take advantage of Mr. Cromey's expertise in this area. Allow us to teach you, your students, staff and post-docs how to correctly work with digital images. You can review a list of image ethics guidelines (Digital Imaging: Ethics) and Mr. Cromey was a contributing author for the Online Learning Tool for Research Integrity and Image Processing (a case-study based learning tool, this site was funded by a grant from the US Office of Research Integrity).
• YouTube videos on using OMERO for image data management.

Other ways to learn more

Visit our award winning Microscopy & Imaging Resources pages (on the UA Microscopy Alliance), or browse our long list of PDF tutorials, tip sheets and handouts (on the UA Microscopy Alliance).

The following opportunities are not specific to the Cellular Imaging Resource, but are available on the UA campus:

• Microscopy-related workshops & seminars are announced regularly on the UA Microscopy Alliance website (a project developed and supported by Mr. Cromey).
• Fundamentals of Light Microscopy & Electronic Imaging - CMM 565A This is a lecture/hands-on course that teaches the essential principles and applications of light microscopy and electronic imaging.  By the end of the course, you will be able to use and adjust a research microscope for various modes of light microscopy. Instructor: Dr. Mouneimne.
• Human Histology - CMM 447/557 (3 units, taught during summer pre-session), This course will provide pre-health science professions students as well as students planning a career in biomedical research with essential background in functional morphology of human tissues and organs. Instructor: Dr. Lybarger
• Pathology 515 - (spring semester) The course is designed for graduate students training for a career in biomedical research. The goal of the course is to expand and extend the student's knowledge of normal structure and function, into the realm of disease processes. Instructor: Dr. Breihl.
• The UA's Edge learning includes a subscription to LinkedIN Learning, which includes thousands of courses, with many on familiar software titles. As part of the campus license for Adobe Creative Cloud, campus users have access to a large collection of tutorials for users of Adobe Creative Cloud.
• UA Office of Student Computing Resources - provides software assistance, and free access to multimedia equipment for UA faculty, staff & students, with access to knowledgeable staff. Also, the UA Library allows campus users can check out computers, tablets, video cameras, lighting, DSLRs, etc.

The facilities affiliated with Cellular Imaging have instruments in a number of locations. These maps will make it easier for users to find the appropriate buildings and rooms. Some buildings require pre-authorized CatCard access.

NOTE: These map links are custom queries that use the University of Arizona's geographic information system (GIS) resources. They highlight specific locations within buildings or buildings within the Tucson campus. Users can zoom out to see the context of where the highlighted rooms are located in relation to other nearby buildings on the campus map.

The Cellular Imaging Facility Core supports the UA Microscopy Alliance website. This includes:

• Microscopy-related resources for Biomedical researchers - as complete a list of microscopy services, instruments, and core facilities for the University of Arizona as can be found anywhere.
• Microscopy & Imaging Resources online - online learning resources for a number of different types of microscopy
• Printable materials - Tutorial & informational PDFs written by Mr. Cromey
• Did you know that? - a collection of imaging-related information about available tools and resources
• YouTube tutorial videos on sample preparation for microscopy and using the OMERO image data management software.