Recent software automates evaluation of calcium release events

A team of UC Davis and University of Oxford researchers have developed an revolutionary tool: SparkMaster 2. The open-source software allows scientists to research normal and abnormal calcium signals in cells routinely.

Calcium is a key signaling molecule in all cells, including muscles like the center. The brand new software enables the automated evaluation of distinct patterns of calcium release in cells. This includes calcium “sparks,” microscopic releases of calcium inside cardiac cells related to irregular heartbeats, also referred to as arrhythmia.

A research article demonstrating the capabilities of SparkMaster 2 was published in Circulation Research.

Jakub Tomek, the primary writer of the research article, is a Sir Henry Wellcome Fellow within the Department of Physiology, Anatomy and Genetics on the University of Oxford. He spent his fellowship 12 months at UC Davis, working with Distinguished Professor Donald M. Bers.

It was great to present SparkMaster 2 at recent conferences and see the enthusiastic response. I felt it will be an outlier and that few people would care. But many individuals were enthusiastic about having a brand new evaluation tool that overcomes lots of the restrictions they’ve experienced with prior tools.”

Jakub Tomek, first writer of the research article

Fellowship at UC Davis results in updated tool

Problems with how and when calcium is released by cells can have an effect on a spread of diseases, including arrhythmia and hypertension. To know the mechanisms behind these diseases, researchers use fluorescent calcium indicators and microscopic imaging that may measure the calcium changes on the cellular level.

Nevertheless, the resulting data files are large and difficult to research by hand, so customized software evaluation tools are essential.

On the Bers Lab at UC Davis, Tomek discussed evaluation tools with Christopher Y. Ko, an assistant project scientist. They identified the necessity for higher, more user-friendly software, which led to the event of SparkMaster 2.

The brand new tool builds upon the success of SparkMaster, which was released in 2007 by Bers and Eckard Picht. Picht is a physician-scientist who worked with Bers, first at Loyola University Chicago after which for just a few years at UC Davis. On the time, there was no user-friendly free software that might analyze calcium sparks -; an important a part of their research -; in order that they developed one.

To create the brand new software, SparkMaster 2, Tomek worked with Bers, Ko, Manuel F. Navedo and Madeline Nieves-Cintron within the Department of Pharmacology on the UC Davis School of Medicine.

Although much of the brand new interface resembles the unique SparkMaster, they began from scratch for the programming. Using Python, an open-source programming language that has grown in popularity, they were in a position to utilize many existing tools and libraries to create the unique features they wanted.

They ended up with software that may analyze calcium sparks recorded using different microscopy approaches and from cells from different tissues and genetically modified mice. Some key features of the new edition include:

• improved user interface
• higher accuracy at identifying calcium release events than previous tools
• ability to discover multiple forms of calcium-release events
• ability to accurately split and analyze individual sparks inside spark clusters

“SparkMaster 2 is even easier to make use of and is far more powerful in the range of event types it will possibly analyze quantitatively -; sparks, waves, mini-waves and latencies. And it has higher accuracy and sensitivity, leading to fewer missed events and fewer erroneous positives,” Bers said.

Bers anticipates the first users of the software will probably be scientists who study calcium in muscle. “Nevertheless it could also be useful for researchers who study other cell types, comparable to neurons, that exhibit local calcium events which are vital in regulating cellular function,” Bers said.

Ko, who’s a co-developer of the brand new tool, can also be focused on the broader research applications for the brand new software.

“I’m particularly excited in regards to the latest scientific questions that SparkMaster 2 will enable the biomedical research community to reply and, in turn, the power to more completely and accurately understand the biology that underlies human physiology in health and disease,” Ko said.

Additional authors on the paper include Nieves-Cintron and Navedo from UC Davis. They were instrumental in demonstrating how the software could be used outside cardiac research, and across distinct cell types, showing its big selection of possible uses.