Workflow that allows for individual analysis of various channels.


Harriet Hu, PRIME 2012 (Australia)

The advent of modern biological microscopy has led to the integration of visualization software with computational tools used to analyze microscopy images. In collaboration with PRIME mentors David Abramson and Ilkay Altintas, as well as Mary Vail from the Department of Biochemistry and Molecular Biology at Monash University, I designed a project to increase efficiency of everyday microscopy analysis. Dr. Vail’s work focuses on the effects of an anti-EphA3 antibody, chIIIA4, and its attenuation of tumour growth in cells (see Figure). Dr. Vail, a biological scientist, noted that conducting routine post-imaging analysis can create a bottleneck effect — much of which can be automated through the use of the Kepler Scientific Workflow System. Kepler is a combined workflow graphical user interface and a background execution engine that assists non-computer scientists in analyzing scientific data. Using Kepler v2.3, as well as the Nimrod/K tools developed at Monash, I was able to construct several workflows that streamlined image processing of experimental data.

Programs such as the LIF2OME, used for image extraction, and ImageJ for image processing were integrated into Kepler workflows, providing greater usability and functionality in image processing. Each workflow can be modified to accept necessary parameters in order to create composite images, analyze particles, and compute individual analysis on separate channels of an image.

In addition, these workflows can be further developed based on the analysis that needs to be conducted per experiment, and provide the foundations for more workflows that can be used for image analysis. This project allowed for future case studies of the functional uses of the Kepler Scientific Workflow System, as well as a continuation for the long-lasting international collaboration between Monash University and the San Diego Supercomputer Center. For more on NimrodK, visit, and for more on Kepler, go to

PARTICIPATING RESEARCHERS: PRIME 2012: Harriet Hu;Monash/MURPA: David Abramson; Monash: Mary Vail; SDSC/UCSD: Ilkay Altintas