Microscopy and Microfluidics Core

The Microscopy and Microfluidics Core of the Center for Cell Signaling in Gastroenterology provides sophisticated cell imaging and microfluidics technologies and applications expertise to support faculty research through three main objectives:

  • Providing reliable, accessible and state-of-the-art microscopy technology and microfluidics devices to faculty members to facilitate their study of digestive diseases-related cellular signaling cascades.
  • Educating and training faculty members in the use of both basic and sophisticated cellular imaging and microfluidics methods.
  • Working collaboratively with faculty members to develop proficiency in the use of optical imaging and microfluidics technologies that offer new capabilities for assessing cell signaling.

Core leadership


The core offers a variety of services, mainly to center faculty members and their laboratory team members. These services include:


  • Experimental study design to make optimal use of available technology.
  • Development of custom applications and protocols.
  • Writing methods sections in grant proposals and manuscripts.

Consults and training

  • Technology.
    • Confocal microscopy.
    • Histology microscopy.
    • Live cell microscopy.
    • Microfluidics devices.
    • Wide-field microscopy.
    • Total internal reflection microscopy (TIRM).
    • Super-resolution microscopy.
  • Applications.
    • High-resolution, real-time imaging of live cells.
    • Confocal microscopy coupled with computer-based 3D image reconstruction.
    • Fluorescence resonance energy transfer (FRET).
    • Fluorescence recovery after photobleaching (FRAP).
    • Expression and use of fluorescence-based bioprobes.
    • Imaging cells in 3D matrix.
    • Deconvolution microscopy.
    • Automated multi-well plate imaging.
    • Data interpretation.

Microscopy equipment

  • Zeiss LSM980 equipped with airy scan super resolution technology.
  • Nikon AXR High-Definition Resonant Scanning Confocal System.
  • Nikon A1R standard confocal microscope.
  • Zeiss Axio-Observer 7 inverted microscope optimized for live cell experimentation.
  • Zeiss Axio Scope A1 upright microscope optimized for standard histological investigations of digestive diseases-related cells and tissues.
  • Zeiss LSM 780 laser scanning confocal.
  • Zeiss LSM 510 laser scanning confocal microscope.

Microscopy reagents

The Microscopy and Microfluidics Core has developed an online list of more than 70 reagents available for free to all C-SiG members. These reagents include:

  • Vital dyes to label ER, mitochondria or lysosomes in living cells.
  • Calcium sensor constructs used to measure calcium in whole cells or within specific organelles.
  • FRET biosensor constructs to measure PKA activity in whole cells or on raft or nonraft membranes.
  • APEX constructs.
  • Tagged constructs to signaling, adhesion and cytoskeletal proteins.
  • Antibodies to cell signaling components.

Microfluidics services

  • Assistance with experimental study design to make optimal use of available technology.
  • Custom device design and fabrication.
  • Technical assistance, including executing experiments.
  • Custom applications and protocol development.
  • Assistance with writing methods sections for microfluidics technologies in grant proposals and manuscripts.

Microfluidics devices

  • Spheroid and organoid culture.
    • Specifications and properties:
      • Spheroids or organoids culturing.
      • Single or multiple cell types.
      • Homogeneous spheroid formation.
      • Constant number of spheroids among testing conditions.
      • Customizable chamber size and number of wells.
    • Functions and applications:
      • Functional assays.
      • Drug testing.
      • Cell injury.
      • Cell-cell interactions, such as immunotherapy.
      • Immunostaining.
  • Organotypic cultures.
    • Specifications and properties:
      • Intact tissue cultures.
      • Suitable for biopsies, resections or organoids.
      • Negligible tissue manipulation.
      • Minimal sample required.
      • Culture chamber is easily accessible.
      • Tissue retrieval capabilities.
    • Functions and applications:
      • Single or multiple tissue cultures or cocultures.
      • Disease modeling.
      • Personalized diagnosis and treatment.
      • Functional assays.
      • Assays capabilities similar to spheroids culture device.
  • Paracrine cocultures.
    • Specifications and properties:
      • Independent culture chambers interconnected by microgrooves.
      • Bidirectional paracrine signaling.
      • Coculture of organoids, such as primary pancreatic islets and hepatocyte spheroids.
    • Functions and applications:
      • Assessment of the effect of paracrine communication.
      • Cell injury in one or both cell types.
      • Drug testing.
      • Cellular fate determination (differentiation).
  • Neuro-epithelial cocultures.
    • Specifications and properties:
      • Independent culture chambers interconnected by microgrooves.
      • Culturing of neurons and planarized organoids.
      • Microgrooves allow for axonal guidance toward planarized cells.
    • Functions and applications:
      • Recreate neuro-epithelial interconnections.
      • Cellular intercommunication assays.
      • Mechanistic or chemical stimuli.
      • Real-time microscopy imaging.

External research access to services

Research teams outside of Mayo Clinic can access select core services as our resources permit. External researchers must be from Digestive Diseases Research Core Centers funded by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). Email us for information.