Research

Imaging Logistics

A Montage of Neurons in a Cleared Tissue

The Microscopy Innovation Lab builds and develops cutting-edge instrumentation meant to tackle challenging biomedical problems. It should be noted that these microscopes are developmental systems and are accompanied with unique challenges. For example, they require expert operation, and typically necessitate advanced image processing and analysis (and therefore some computer programming). Below we mention some of these logistics.

Sample Preparation
  • The sample preparation (clearing, mounting, labeling, etc.) should be optimized using commercial microscopes available in the Live Cell Imaging Facility.
  • The microscopes in the Microscopy Innovation Lab can only accommodate specific sample sizes and geometries. Also, the quantity of samples to be imaged needs to be considered.
  • If a specific subset of the tissue is of interest, the user will need to be present to help identify these regions.
  • User should provide us with clear directions on how to store the sample, as to whether the signal/sample will decay over time.
  • Many of the microscopes require a significant volume of immersion media (upwards of ~90 mL).
Computational Demands 
  • These microscopes can routinely generate multiple terabytes of data, and thus require high-performance computing.
  • All of the image processing tools that have been developed for Linux operating systems and are available on BioHPC.
  • Data will be collected by the Advanced Imaging Initiative, processed if necessary, and then the end-user will need to copy that data to their own directory on BioHPC or an equivalent file system. Data not copied within a week of notification will be deleted automatically.
  • Maintaining your own data systems is not recommended. Hard-drive failure is common when operating large data storage systems, which increases the chance of data loss.
  • A high-performance Windows workstation is available for a fee on an hourly basis for visualization of imaging data with leading commercial software packages, including Arivis, Imaris, ImageJ, and MATLAB.