How open-source software could finally get microscopes speaking the same language #Science @Nature
In a xkcd strip published in 2011, cartoonist Randall Munroe pokes fun at people’s inability to develop a universal standard for, say, electrical outlets, printer-paper dimensions or TV remote-control signals. From 14 competing standards in the opening panel, the desire to create a ‘universal’ standard inevitably just adds one more to the stack (https://xkcd.com/927).
“That comic is shown at almost every presentation I attend,” says Swedlow, a cell biologist at the University of Dundee, UK.
Swedlow has been working for two decades to standardize image formats for biological microscopy data. During that time, the number of standard file formats in the field has proliferated to around 160. Now, thanks to a project in which Swedlow has a leading role, there is one more. “For 20 years we’ve been trying to solve this file-format problem,” he says. “And how are we going to solve it? Come up with a new one.”
OME-Zarr is a blend of two projects. The first is the Open Microscopy Environment (OME), which Swedlow started in 2002 to develop an open-source specification for biological microscopy data. Zarr is a newer creation: a method for optimizing how large data arrays are stored in, and downloaded from, the cloud.
Check out how this project is looking to unify scientific data in the Nature article here.
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