The macroscope is a larger version of a microscope and will enable researchers to see how clots develop and break down in real-time.
"This is really exciting because we haven't been able to do this before," Dr Jessica Maclean, from the Heart Research Institute, said.
"We get to see how clots form, how they change over time and how treatments work," she said.
Blood clots account for 85 per cent of all strokes, which affect 55,000 Australians each year.
Researchers are on the search for more effective treatments, as the standard clot-busting drug is safe for only 10 per cent of patients.
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"Finding something that can break down the whole clot can prevent it from re-forming and also not cause damage to the brain is really important," Dr Maclean said.
The macroscope allows scientists to use fluorescent markers to identify and track the activity of the particles of a blood clot.
The Heart Research Institute says the macroscope, which costs $30,000, is on the top of its wish list this Christmas to help advance discoveries.
"Move it forward so we can develop safe and effective treatments," Dr Maclean said.