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New initiative aims to improve open-source software

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06/28/22 | New initiative aims to improve open-source software

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The Open Science Software Initiative will help Janelia scientists develop and maintain software for biological research.

 

In the two years since Carsen Stringer released the computer program Cellpose, it has been used by hundreds of biologists around the world to map the boundaries of cells. The software can pick out many kinds of cells in microscope images and has been a game changer for biologists who might otherwise spend weeks mapping cells by hand or building their own software.

But, like any popular computer program, users want updates and new features. They can post these requests – which range from fixes to additions for their specific needs – on GitHub, where the open-source software is freely available.

Sometimes another software developer will make these updates, but more often the task falls to Stringer, who fits in work on the more popular requests when she has time outside of her job as a group leader at Janelia. In most cases, the requests come from biologists who don’t have the expertise to make their own updates.

“There is no prize for other developers to contribute to my software,” Stringer says. “Unless it is going to change your life as a biologist, then people aren’t going to add it. But often the people who need those additions are the biologists themselves, who don’t have extensive software experience.”

The new Open Science Software Initiative aims to solve this problem by supporting Janelia scientists with development and maintenance of their software. By providing dedicated software developers, the new initiative will benefit Janelia scientists by freeing them up to work on new projects and the entire scientific community using these tools by providing needed updates, says Stephan Preibisch, director of Janelia’s scientific computing software team, who is spearheading the new initiative. In many cases, these custom, one-of-a-kind computer programs are used by hundreds of biology labs worldwide.

Cellpose is one of a dozen projects the new initiative is supporting at its outset. In some cases, as with Cellpose, software engineers hired through the program will help maintain and extend the software. In other cases, engineers will help labs develop new open-source software, such as a program that uses deep learning to detect single molecules.

The idea to create the Open Science Software Initiative grew out of discussions between Preibisch, Senior Group Leader Kristin Branson, Group Leader and Interim Head of Computation and Theory Stephan Saalfeld, Senior Director of Scientific Operations Reed George, and Executive Director Ron Vale. They saw the need for a program to support Janelia scientists with maintenance and development of their software.

“There are labs who develop this really amazing software that is used by thousands of people, but maintaining it is a huge effort,” Preibisch says. “Then, there are other labs who develop these great algorithms, but they are theoreticians; they see that one could make this into a software that could potentially be very useful, but it is outside their expertise to do that.”  

The new initiative reflects Janelia’s overall commitment to open science and creating freely available products that benefit the entire scientific community, Preibisch says. It also has the potential to accelerate science, by enabling more people to use the software while also freeing up Janelia scientists to develop new programs, he says.  

“How horrible would it be if everyone writes their own software instead of sharing it? Open software focuses on things that many labs need, so there are a lot of positive benefits for the entire community – they don’t have to start from scratch,” Preibisch says. “At the end of the day, this makes research possible because people can immediately focus on the actual questions.”