Shared Core Facilities
Confocal Imaging Core

Confocal Microscope Instrumentation, Training, and Consult

The primary mission of the Confocal Imaging Core is to provide cost-effective access to high-end imaging devices and the expertise to utilize the microscopes. The CIC offers a variety of services to aid researchers in acquiring and analyzing optical microscopy data. From experimental consultation to final analysis, the core is there every step of the way.

Techniques and Services


  • Confocal laser scanning microscopy
  • High-speed single photon confocal laser scanning microscopy
  • Multi-photon confocal laser scanning microscopy
  • Wide-field
  • High speed spinning disk confocal with optical reassignment super resolution

Technical Capabilities

  • Live imaging of cells, tissues, and animals
  • Stochastic Optical Reconstruction Microscopy (STORM) super-resolution
  • Total Internal Reflectance Microscopy (TIRF)
  • Fluorescence Recovery After Photobleaching (FRAP) microscopy
  • Calcium imaging
  • Multiplexing (up to 8 channels)


If you are interested in being trained on one the systems complete the Stratocore form:

Training sessions have two parts- the first session is on Microsoft teams and the second session is on the microscope with your prepared sample. Trainings are bimonthly on teams and based on the availability of the staff and instrument. There is no cost for training. See below for steps to initiate training.

CCHMC internal: follow this link to complete the training request form.

External users: send us an email to start the process,

Advanced Image Analysis

The CIC offers training and assistance with data collected in the CIC. Currently, we have nine image analysis workstations: all have NIS-Elements, and five are designated for Bitplane Imaris. Some have advanced features such as trainable artificial intelligence, denoising, object tracking, deconvolution and batch processing. Training is not required before booking advanced image analysis workstations.

Sample Preparation

We can assist with a variety of sample preparation techniques to increase resolution, including tissue clearing for large samples and expansion for sub-optical resolution.

Tissue clearing methods remove lipids to increase light penetration and increase resolution with larger samples. We provide training on a variety of passive and active tissue clearing techniques, including Spalteholz-like methods (BABB, DISCO, PEGASOS), aqueous methods (PACT, CLARITY, Ce3D), and newly developed protocols such as EZ Clear. Additionally, we maintain a Logos Biosystems X-Clarity machine if needed.

Expansion microscopy isotropically expands samples embedded in a hydrogel 4-10xs. This method is best utilized for biological phenomenon below the diffraction limit of light.

Please contact us if you have any sample preparation questions for your optical microscopy.


If you have any questions about optical microscopy please feel free to contact us for more information.