Blog Page


It takes two: Methods for analyzing neural activity from calcium imaging – Medical Xpress

Forget Password?
Learn more
share this!
January 3, 2023
by Sara Vaccar, Carnegie Mellon University, Department of Biomedical Engineering,
A growing body of researchers is utilizing optical imaging to monitor activity in the brain. One type of optical imaging, two-photon calcium imaging, has been widely adopted for its ability to record large neural populations. A major outstanding question, though, is which statistical methods to use to analyze calcium imaging recordings.

“Prior to our work, two standard types of were applied to imaging recordings—deconvolution and dimensionality reduction,” explained Steve Chase, professor of biomedical engineering at Carnegie Mellon and the Neuroscience Institute. “After testing each technique using a collection of simulated and laboratory data, we concluded that it didn’t make sense to do either/or. Combining the approaches into one operation proved to be more successful.”
Carnegie Mellon University and Howard Hughes Medical Institute researchers teamed up to analyze existing methods being used to interpret calcium imaging recordings, as well as propose a novel method that combines two leading approaches. The group’s new method, which performs deconvolution and dimensionality reduction simultaneously, is known as Calcium Imaging Linear Dynamical System or CILDS.
“Through this process, we realized that current methods were often focused on the activity of one neuron, but because we know neurons carry and communicate important information about one another, we wanted to develop a method that examined populations of neurons to better summarize ,” said Tze Hui Koh, first author of the paper and Carnegie Mellon biomedical engineering graduate student. “In the range of situations that we tested CILDS in, it outperformed other stand-alone methods.”
Understanding the different tradeoffs and choices needed to combine deconvolution and dimensionality reduction is another key learning detailed in a recent Nature Computational Science paper. CILDS represents something greater than the sum of its parts.
“We’ve developed a tool and published a paper that shows it’s useful,” concluded Byron Yu, professor of biomedical engineering and electrical and computer engineering. “We have code that is now publicly available, and our goal is for the broader field to do science and discover something about the brain with it.”

More information: Tze Hui Koh et al, Dimensionality reduction of calcium-imaged neuronal population activity, Nature Computational Science (2022). DOI: 10.1038/s43588-022-00390-2

Journal information: Nature Computational Science

Citation: It takes two: Methods for analyzing neural activity from calcium imaging (2023, January 3) retrieved 3 January 2023 from
This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.

Explore further
Feedback to editors
Dec 30, 2022
Dec 29, 2022
Dec 29, 2022
Dec 28, 2022
Dec 27, 2022
2 hours ago
3 hours ago
3 hours ago
3 hours ago
3 hours ago
3 hours ago
3 hours ago
5 hours ago
5 hours ago
6 hours ago
Aug 18, 2022
Jul 21, 2021
Dec 15, 2022
Oct 13, 2021
Jul 29, 2022
Mar 1, 2022
6 hours ago
7 hours ago
7 hours ago
8 hours ago
12 hours ago
12 hours ago
Use this form if you have come across a typo, inaccuracy or would like to send an edit request for the content on this page. For general inquiries, please use our contact form. For general feedback, use the public comments section below (please adhere to guidelines).
Please select the most appropriate category to facilitate processing of your request
Thank you for taking time to provide your feedback to the editors.
Your feedback is important to us. However, we do not guarantee individual replies due to the high volume of messages.
Your email address is used only to let the recipient know who sent the email. Neither your address nor the recipient’s address will be used for any other purpose. The information you enter will appear in your e-mail message and is not retained by Medical Xpress in any form.

Get weekly and/or daily updates delivered to your inbox. You can unsubscribe at any time and we’ll never share your details to third parties.
More information Privacy policy
Daily science news on research developments and the latest scientific innovations
The latest engineering, electronics and technology advances
The most comprehensive sci-tech news coverage on the web
This site uses cookies to assist with navigation, analyse your use of our services, collect data for ads personalisation and provide content from third parties. By using our site, you acknowledge that you have read and understand our Privacy Policy and Terms of Use.