The University of Cambridge researchers needed a data analysis solution that would allow them to dynamically visualize cell movements over time.

A central challenge in developmental biology is the study of how cells reorganize during an embryo's development. Cells reorganize from a mass into an organized structure throughout an embryo's gestation. Each mass of cells follows a set of instructions for which body part it is to become, developing from a sheet-like layer of cells into the recognizable structures that eventually become functioning parts of the body.

IDL has been used for nearly 30 years to analyze and visualize medical images for various purposes - from detecting disease to teaching students about human anatomy. Now, biologists at Cambridge are using IDL to study problems in developmental biology. Advanced imaging techniques and sophisticated data analysis programs like IDL now allow researchers to solve the fundamental mysteries of human development.

Researching biologists, including Richard Adams and Guy Blanchard at the University's Department of Physiology Development and Neuroscience, are particularly interested in understanding the dynamics of these cell movements - or morphogenesis. They hope to understand how these processes proceed in the normal embryo, and how errors can cause some cells to develop abnormally, for instance, those resulting in neural tube defects.

Adams and Blanchard use time lapse imaging to study embryonic cell development of the zebrafish - a popular model that develops rapidly, allowing scientists to study full life cycles over a short period of time. To collect data, zebrafish embryos are placed on confocal microscopes, which are used to obtain high resolution, 3D images of the thick specimens. Embryos are then injected with fluorescent dyes which stain different kinds of cells or regions of cells, making their morphology - or reorganization - easy to track.

To monitor cell behavior over time, Adams and Blanchard used IDL to develop several custom software applications that manage the enormous amounts of confocal data, and to create movies tracking individual cell movement. Adams chose IDL because he says he "wanted a tool that had gave access to the mathematical functions that we needed, and allowed me to perform everyday tasks such as displaying an image without writing lots of code." The lab's custom applications allow the participating biologists to isolate and slice and dice data, pick subsets of that data, reconstruct slices into 3D models, and ultimately generate movies following cell development.

The lab is visited frequently by many collaborators who use Adams' and Blanchard's IDL-based programs, so they are designed to be as user friendly as possible. IDL's widgets and other built-in functionality allow the team to easily create familiar ease-of-use functionality, such as buttons, sliders and icons. Visitors can use the applications to easily manipulate and animate their own data.

Blanchard is currently developing an IDL application that takes the research one step further. It automatically identifies cells in the movies and follows and analyzes their changes over time. "IDL allowed us to incorporate sophisticated algorithms, create routines to easily track cell movements, look at shape changes, and to visualize our data effectively," said Adams. "Before, I had to spend a lot of time writing code to do my job, rather than concentrating on the science.

• The lab's custom applications allow the participating biologists to isolate and slice and dice data, pick subsets of that data, reconstruct slices into 3D models, and ultimately generate
• movies following cell development
• Before IDL they had to spend a lot of time writing code to do their jobs, rather than concentrating on the science
• IDL allows the researchers to easily track cell movements, look at shape changes, and to visualize data effectivley