The combination of modern microscopy and DNA techniques has revolutionized brain research over the past 10 years. It is now possible to visualize the activity of hundreds of individual brain cells in mice during behavioral tasks. This can be done over periods of weeks to months, showing how brain cells process information and how this changes as the animals learn.
One of the most powerful ways to do this is by introducing DNA into brain cells that encodes a fluorescent protein. This protein changes fluorescence intensity when it binds to calcium. Since calcium enters the cells when they are active, changes in fluorescence indicate firing of the brain cells.
A special microscope that can image deep into the brain allows monitoring of these changes in light intensity. This results in hours-long movies of hundreds of brain firing cells. Understandably, it is a major challenge to analyse this information. Smart software is needed to automatically identify the brain cells (or their neurites), isolate their signals, filter out noise, and to find back the same brain cells on different days.
Several software tools are available that perform some of these tasks, but they are not always intuitive or user-friendly and do not offer all the necessary features in one package. Therefore, Leander de Kraker and Chris van der Togt have created a software tool in the Levelt lab that performs all these tasks and is easy to use. The software has been extensively tested and described in an article published in Cell Reports Methods.