In order to understand how the brain functions, we have to be able to track the movement and activity of individual neurons. This is maddeningly complex at present, as single neural cells have to be visually tracked by grumpy lab techs to understand even a tiny bit of what’s going on. Now a new tool called CalmAn, developed at the Flatiron Institute in New York City, has been verified to track large numbers of neurons at the same time.

The system relies in part on machine-learning methods to follow the cells along as they move under the microscope. In a study, the results of which were published in journal eLife, the system was nearly as good as trained humans at tracking cells from calcium imaging data.

The technique is already being used by dozens of labs and the latest study will allow more institutions to feel confident about implementing this technology in their studies. This will hopefully speed up neuroscience research and lead to therapies and cures for a variety of conditions.

Image: An image of neurons (white) taken using calcium imaging techniques. An innovative software dubbed CaImAn can automatically differentiate between individual neurons (yellow outlines) with nearly the same accuracy as a human (red outlines). Giovannucci et al./eLife 2019

Study in journal eLife: CaImAn an open source tool for scalable calcium imaging data analysi…

Download the tool for free on GitHub: CaImAn…

Via: Flatiron Institute…



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