Single Cell Phenomics Center



The Single Cell Phenomics Center is new to Iowa State University.  Utilizing the latest advances in image-based flow cytometry, the Single Cell Phenomics Center can collaborate on a range of research topics and is a cornerstone in the multiomic era.  Rather than a traditional flow cytometer, the technology can be likened to a high-throughput microscope, imaging thousands of cells in seconds.  We can image cells simultaneously in brightfield, side scatter, and a large range of the fluorescent palette at 20/40/60x objectives along with extended depth of field (EDF) capabilities. Cells can range from 120 μm wide by 200 μm or as small as extracellular vesicles (EVs) and virus particles. Data can be analyzed performing traditional flow cytometry methods (.fcs file type) or more advanced image-based flow cytometry methods incorporating machine and deep learning artificial intelligence methods.

Combining the Best of Flow Cytometry and Fluorescence Microscopy

IBFC combo
Source: Luminex


Broad Range of Research Applications

The powerful combination of quantitative image analysis and flow cytometry in a single platform creates exceptional new experimental capabilities. The following are examples of areas where the ImageStreamX Mk II imaging flow cytometer can bring more power and insights into your research; however, the possibilities are endless.

Imaging flow cytometry enables applications that cannot be performed by flow cytometry or microscopy alone.
Emerging Applications
Source: Luminex

Introduction to Image-based Flow Cytometry

Artificial Intelligence: Machine & Deep Learning

Image outputs from image-based flow cytometry can easily incorporate machine & deep learning analysis.

convolutional layers
Source: Doan et al., 2018. Trends in Biotechnology. DOI:10.1016/j.tibtech.2017.12.008


T-SNE visualization
T-SNE visualization of label-free cell training data set. Source: Nassar et al., 2019. Cytometry Part A. DOI:10.1002/cyto.a.23794


Our Recent Publications Utilizing Image-based Flow Cytometry:

  • Zinc ion flux during mammalian sperm capacitation, Kerns et al., 2018. Nature Communications
  • Compartmentalization of the proteasome-interacting proteins during sperm capacitation, Zigo et al., 2019. Scientific Reports
  • Pharmacologic treatment with CPI-613 and PS48 decreases mitochondrial membrane potential and increases quantity of autolysosomes in porcine fibroblasts, Mordhorst et al., 2019. Scientific Reports.
  • Reciprocal surface expression of arylsulfatase A and ubiquitin in normal and defective mammalian spermatozoa, Kelsey et al., 2020. Cell and Tissue Research
  • Relationship between the Length of Sperm Tail Mitochondrial Sheath and Fertility Traits in Boars Used for Artificial Insemination, Kerns et al., 2020. Antioxidants
  • Sperm Cohort-Specific Zinc Signature Acquisition and Capacitation-Induced Zinc Flux Regulate Sperm-Oviduct and Sperm-Zona Pellucida Interactions, Kerns et al., 2020. International Journal of Molecular Sciences.

Other's Publications Utilizing Image-Based Flow Cytometry:

Want more information?

Services are available internally to ISU principal investigator labs and to external stakeholders.  For sample preparation details, click HERE.  For more information about the ImageStream Mark II, click HERE or contact the center's director HERE.


Internal and External Sample Scheduling

We make use of iLab for equipment scheduling and facilitating billing.  To schedule, you must first create an iLab account and associate that with your PI.  Please register for an account following the SOP’s below. You can find the website through your Okta portal (you can add the iLab app) or here:

For an up to date SOP, please look here:

Or alternatively, go to Learn@ISU and search for the course titled "Internal Customer Access and Use of iLab" and follow the directions there.

After you have created these accounts, schedule your samples via the iLab scheduler:

If you have any questions on this process, contact the center's director HERE.