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Celebrating 45 Years of Advancing University of Iowa Research


The University of Iowa's Central Microscopy Research Facility provides a wide variety of microscopy techniques for biomedical investigators, an experienced staff, and support for the beginner and experienced investigator. As one of the best equipped university core microscopy facilities in the nation, our microscopy team is ready to fully support your research program.


-------------------- CMRF News -------------------


Due to the increase in local infection rates the CMRF has updated its COVID protocols:


With an increase of COVID positive tests in Johnson County, the CMRF will now be accessible by appointment only.  Face masks use is encouraged in the facility.  Please contact a Staff member for how we can assist you with your research needs.  Thank you for your understanding during these novel times

Investigators may continue to schedule CMRF resources on their own through Calpendo.

Investigators approved for after hours access can continue to reserve and use equipment outside of 8-5 M-F.

Face shields are not required.

Note: If working with chemicals or using a microtome you must bring a lab coat.


 Calpendo Reservation App Update


The CMRF is transitioning to Calpendo, an integrated scheduling and invoicing application that coordinates resource reservation, usage and billing.

All CMRF investigators must create a User account by going to, clicking on the "Register new User" button then the "HawkID login" button. You must fill out every field in your User Profile.

This is reminder that all CMRF investigators need create a project by July 1st. On that day you be able to reserve CMRF Resources on your own without going through your CMRF staff contact.

Please log into Calpendo and go to ProjectsàCreate Project and fill out all fields. Most of the fields are mandatory. Only include resources on which you have been trained. These will be confirmed by your CMRF staff contact. Email them if you have questions regarding resource access.

If you use more than one MFK in your research you will need to create a separate project for each one. When User scheduling opens up you will need to select the project relevant to the specific work you will be doing during the reservation.

When creating a Project in Calpendo, entering the proper 40 digit MFK number can be a bit confusing. Please use image below as a guide. It shows how the 40 numerals are distributed.


  • Some of the fields in your MFK may be empty. If so, enter the proper number of zeros for that field
  • For the 4-digit Iacct field you should enter 6218 (as shown in the image)
  • When entering the MKF there should be no spaces, just a single string of 40 digits
  • If you are using a VA account and don't have an MFK, enter "NO-MFK" in the MFK field
  • Please contact Lucy or Tom if you have any questions


CMRF resource billing continues to be based on the reservation time or instrument usage time, whichever is larger, with a minimum reservation time of 15 or 30 minutes, depending upon the instrument. 


The CMRF Announces the Purchase of a state-of-the-art Zeiss LSM 980 AiryScan 2 Confocal Microscope


The CMRF recently installed an inverted Zeiss LSM 980 AiryScan 2 confocal microscope. This next-generation confocal has improved speed, sensitivity, and resolution. The AiryScan 2 detector and Multiplex upgrade deliver fast, consistent, and quantitative Supperresolution. The system has full environmental control to support live-cell imaging experiments, while also having the capability to image standard cover-slipped slides.



Key features of the system include:


  • 2 liquid-cooled MA-PMT detectors and 1 high-sensitivity 32-channel GaAsP array detector with full emission tunability
  • AiryScan 2 superresolution detector, enabling 120 nm resolution in XY, 350 nm in Z, works with all available lasers, and doubles as an additional GaAsP confocal detector
  • High-speed Z-piezo stage for fast volume imaging
  • Observer 7 inverted stand optimized for long-term live-cell imaging with automated scanning stage, full environmental control (temperature, CO2, humidity) and Definite Focus 2 focus-maintaining system
  • Argon and diode laser lines 405, 445, 488, 514, 561, 594 and 639 nm
  • ZEN 3.2 software package including modules for Z-stack, time-lapse, photobleaching/photoactivation, spectral unmixing, automated image analysis, FRET, colocalization, autofocus, 3D rendering, tiles and ratiometric tools
  • Transmitted light detector
  • Full set of objectives includes 10x/0.3, 20x/0.8, 40x/1.2 water, 40x/1.3 oil, 63x/1.4 oil


Talk to your CMRF staff contact for more information and to arrange a demo or training.


10X Visium Spacial Transcription Service Available



Leica SP8 Confocal-STED Super-resolution System Upgraded

775 nm Depletion Laser Added

The CMRF’s Leica Stimulated Emission Depletion (STED) super-resolution imaging system, based on an SP8 laser scanning confocal microscope, has recently been upgraded. STED delivers resolution beyond the theoretical limit of light, and fills the resolution gap between standard confocal and electron microscopy. The system now features a 775 nm pulsed depletion laser, in addition to the existing 660 nm depletion laser. This addition will simplify multiple label STED experiments, increase resolution (<40 nm), and reduce photobleaching. The STED system also now features a 93x glycerol lens that will facilitate imaging at greater depth. Follow this link for more information on the system, and sample preparation guides.

Below is an example of the dramatic increase in resolution provided by STED. The sample is 23 nm beads labeled with ATTO647N (top two images) and Alexa 594. Confocal images on the left, 775 nm STED on the right. Note the typical diffraction-limited 200 nm spots in the confocal images, and the dramatic resolution improvement in the STED images.

647N-AF594 STED


FRAP and FRET Wizard Installed on Leica SP8 Confocal/STED

Also, the CMRF has upgraded the Leica SP8 Confocal/STED microscope with FRAP and FRET software. The new modules use a “Wizard” format to guide you through configuration and data collection. FRAP and FRET software guides can be found on the SP8 website.


 High-end Workstation for Huygen's Pro Deconvolution and Imaris 3D and 4D Real-time Interactive Visualization and Analysis Software.



To process, analyze and visualize STED and confocal data sets, the CMRF maintains current copies of SVI’s Huygen’s Pro and Oxford’s Imaris. Huygen’s is the gold standard deconvolution app, increasing resolution and removing noise from confocal and STED z-stacks. Imaris is the world’s leading 3D-4D image visualization and analysis package, providing sophisticated, easy-to-use volume, distance and tracking modules. Both apps are installed on a custom-built high-end PC workstation.

Huygen's Pro features easy-to-use wizards that guide the user through the deconvolution process. Background flare is removed, and resolution can be be improved by 2x.

With just a few steps, Imaris delivers quantitative volumetric and motion-analysis results. Custom Imaris modules are available for neuroscience, (e.g. dendrite and spine analysis,) and co-localization studies. Other available features include:

  • Imaris Measurement Pro: Shape, size and intensity-based quantification.
  • Imaris Track: Imaging, tracking and motion analysis of live cells and moving objects in 2D and 3D.
  • Imaris Filament Tracer: Automatic detection of neurons (dendritic trees, axons and spines,) microtubules, and other filament-like structures in 2D, 3D and 4D.
  • Imaris Coloc: Quantify and document co-distribution of multiple stained biological components.
  • Imaris Cell: Quantitatively examine micro relationships that exist within and between cells.
  • Imaris Vantage: Compare and contrast experimental groups by visualizing image data in five dimensions as uni- or multi-variate scatterplots.


New Paraffin Processor

The CMRF recently installed a Tissue-Tek® VIP® 6 AI Vacuum Infiltration Paraffin Processor. This state-of-the-art system provides reproducible, high-quality processing of histological samples into paraffin.  For more information, contact Chantal at

paraffin processor


High-Resolution Iridium Sputter Coater Available!

The CMRF has purchased a Quorum Technologies 150T ES Iridium sputter coater to support high-resolution SEM imaging. It is capable of producing coatings that are much thinner than standard Au/Pd sputter coating, which can result in higher-resolution images. The QT 150T ES is the ideal coating system for routine imaging above 50,000x. Contact CMRF staff if you are interested in using this instrument.

Office of the Vice President for Research  article on the 2016 Art in Science Contest


CMRF Staff are available  Monday through Friday 8am-5pm and will be happy to assist you! Call 335-8142 or email Randy Nessler for more information.