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Biomedical Image Analysis

The facility allows for analysis of images obtained from Microscopy, Bio-Imaging, Flow Cytometry, Cell Sorting and Ultrasound instrumentation, located on the 3rd floor of Botterell Hall and the Animal Care facilities. We offer instrument access and training, full sample analysis with experienced operators, and experimental troubleshoting/protocol design.

We currently have 2 dual monitor image analysis packages, Image Pro Plus and Metamorph which are available for facility users to take advantage of in their research. Both packages are extremely comprehensive in their image processing, measurement and statistics generation ability and have many versatile analysis plug ins and inbuilt functions.


There are too many image analysis applicatons to list all of them, so if you have a specific request or need please contact Matt or Jeff for advice, however here are some of the more commonly used processes or analysis plugins.


  • Colocalization: The assessment of colocalization of 2 or more individually labelled targets of interest is extremely powerful whether simply wanting to know if a given protein is found in a specific organelle, or if there is specific interaction between targets of interests. We have multiple modalities of differing specificity to offer. At a simple visual level, the overlaying of two or more labels with a colour combination enhancement, (ie green + red = yellow as seen in the below image) can give a basic indication of association between targets of interest. this can be further numerated by use of the Pearson Correlation coefficient which will actually quantify the colocalization based on signal intensity and pixel matching across the whole image, or region of interest. This article based on Image J Colocalization plugins using Pearson’s or Mader’s colocalization coefficients, is an extremely informative read. Strongly recommended.
  • Signal Intensity: Measurements of signal intensity are commonly performed and can be assessed in a variety of ways. This quantification can also be performed on stacks and time lapse sequences/videos to map changes in intensity over time or though the z axes of a 3D model.
  • Object tracking: Both image pro and metaorph have integrated object tracking plug ins that make the assessment of sample dynamics easy to perform. Tracking can be done manually in a point-and-click fashion per frame, or can also be set up to monitor individual objects automatically. Tracking can be performed on multiple objects of interest in an image sequence, and dynamic spatial data (distance, speed, direction etc) generated for further analysis.
  • 3D reconstructions: Part of the power of confocal microsopy is the ability to easily acquire stacks of specific focal planesthat can then be re rendered into high resolution 3d models. Both of the facility IA packages come with this capability and the user has a choice of XY-XZ-YZ representations, with the ability to specify planes and depths of interest.
  • Image enhancement: with the use of common filters, and deconvolution we have multiple means to "clean" images that might appear fuzzy or indisctinct, this example below idemonstrates the cropping of a section of an image of interest followed by the application of a "find edges" filter, to highlight object boundaries.




Image Analysis (independent use)


Image Analysis (with assistance)


Unspecified Technical Assistance




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Botterell Hall 3rd Floor and Animal Care Facilities



If you have any questions please contact Xiaohu Yan (; ext 78265) or Zhilin Chen (; ext. 78238)