Biologists LEVER knowledge from 3D visualisation

Engineers at Drexel University in Philadelphia have developed software that lets biologists identify, tag and track live cells in 3D. 

Dr Andrew Cohen, an associate professor of electrical and computer engineering in the College of Engineering, is leading a group of researchers who are developing the software and hardware that will enable biologists to better track and study the movement and multiplication of cells.

Their goal is to enhance the current visual data that these scientists are working with so that it’s easier to identify changes in cells over time –information that is key to studying the abnormal cell proliferation that causes cancer and also to using stem cells in regenerative medicine.

‘This type of imaging is so important because it allows us to see and measure relationships between cells and their environment,’ Cohen said in a statement.

Typically the process of tracking cell lineage over time requires biologists to watch the time-lapse images and note by hand when the cells multiply –creating a graphic representation of cell division over time called a ‘lineage tree.’ This process, however, can take a researcher several hours.

The LEVER (Lineage Editing and Validation) software lets the researcher work with the computer to delineate cells, colour code them and denote the exact moment of their division. According to the university, LEVER is easier and more accurate than processing the data manually and also provides more data than what can be obtained by hand.

‘It’s like Photoshop for cell biologists,’ Cohen said. ‘The software outlines cells and blood vessels, keeping track of them as they’re dividing and moving around one another. This provides a wealth of information on the patterns of cell shape, motion and division. Visualisation of the 3D microscopy data together with the analysis results is a key step to measure and ultimately understand what drives these cells.’

With an enhanced version of the program called LEVER 3D, which compiles data from multi-layered microscopic images, Cohen’s team can produce a three-dimensional rendering of the cells and animate it through time to show their multiplication and movement. The enhanced imaging gives researchers a unique view of the interaction of stem cells with their surroundings.

By running the software on a computer with a graphics card optimised for gaming and wearing a set of 3D gaming glasses, the program can take scientists inside the microscopic cross section.

In a portion of Cohen’s lab modified to be a viewing theatre, a stereovision projector brings the three-dimensional image data to life. Users can rotate and zoom in and out of the projected image in true 3D, giving scientists vantage points that are not possible when looking through a microscope.

‘LEVER 3D is amazing, it opens new vistas for understanding the stem cell niche,’ said Dr Sally Temple, a cell biologist at the Neural Stem Cell Institute in Rensselaer, New York who has been using Cohen’s software, through the course of its development, as part of her stem cell research since 2005.

Cohen’s goal is to make the software open-source and readily available to any scientists who can use it for their research.

The project, which is funded by the National Institute on Ageing, was recently presented by Eric Wait, a doctoral researcher in Cohen’s lab, at the Symposium on Biological Data Visualisation in Boston. The team plans to enhance the interactive capabilities of the system in order to increase its utility as a tool for research.

Cohen’s work was recently published in the journal BMC Bioinformatics