Spark Analysis Detection

Source Code / Test Data

The material here is based on the algorithm described in Mark-Anthony Bray, Nicholas A. Geisse and Kevin Kit Parker, “Multidimensional detection and analysis of Ca2+ sparks in cardiac myocytes,” Biophysical Journal, 92(12): pg 4433 – 4443 [Link].

Movie (supplemental data) – Movie recorded from an isotropic monolayer of neonatal rat cardiac myocytes, loaded with the Ca2+ sensitive dye Fluo-4. The tissue exhibits several tissue-wide calcium transients, accompanied by spark activity.
(Quicktime, Download).

Available Files

  • Distribution details, including specifics of the files available (Download).
    Please see the distribution file for details on the source code and the format and contents of the test data.
  • MATLAB source code and GPL for spark detection (Download).
  • Spark synthetic data with uniform background flourescence. (Download). ZIP file, 65.6 MB.
  • Spark synthetic data with Ca2+ reuptake background flourescence. (Download). ZIP file, 65.6 MB.

License

This toolbox is released under the GNU General Public License (GPL, see http://www.gnu.org/licenses/gpl.html). This is a copyleft license, which means you have the freedom to use, distribute and modify the code, but only on the condition that you must pass on this freedom. You can integrate this code into proprietary packages, but you must do so according to this rule. That is, some parts of your proprietary package will not have this freedom, but those parts derived from this code must retain that freedom. You must use, distribute and develop the code herein in accordance with the GPL.

Grp_photo_Jan 2014_305W_230H

What's New

Congratulations to John Ferrier for winning the 2017 LG UltraWide Festival October 18th, 2017

The DBG would like to congratulate one of our lab managers, John Ferrier, on winning the 2017 LG UltraWide Festival which was hosted by Linus Tech Tips and Austin Evans!

DBG Nanofibers Merge with Art by Carla Ciuffo August 23rd, 2017

The Disease Biophysics Group would like to congratulate and thank Tennessee based artist Carla Ciuffo in her efforts to integrate our nanofibers into her art exhibit “Cosmic Garden” at Tinney Contemporary, opening this Saturday.

“Tundra,” 2017, polished acrylic with floating museum back frame, 48×48 on display at Tinney Contemporary. (Photo: Photo courtesy of the gallery)

Thank you to our Summer Students! August 16th, 2017

Thank you to all the undergraduate students who spent time working in the lab over the summer. We wish you all the best this school year!

 

Jenny Wang, United States Military Academy at West Point
Daniel Gray, United States Military Academy at West Point
Nikita Pereverzin, United States Military Academy at West Point
Kathryn Dula, United States Military Academy at West Point
Daniel Drennan, Nicholls State University
Michael Ferris, James Madison University
Karla Rivera, Barry University
John Doyle, University of Massachusetts at Lowell
Madeleine Dahl, Salem State University
Nikita Budnik, McGill University
Karaghen Hudson, Harvard University
Sayo Eweje, Harvard University
Michael Peters, Harvard University
Gabriela Berner, Harvard University

Welcome Dr. Ardoña! August 15th, 2017

The DBG would like to extend a warm welcome to our newest postdoctoral fellow, Dr. Herdeline Ardoña. Herdeline recently completed her Ph.D. in Chemistry at Johns Hopkins University,  where she was a part of Prof. Tovar’s lab.  Welcome, Herdeline!

Welcome Dr. Liu! June 23rd, 2017

The DBG would like to extend a warm welcome to our newest postdoctoral fellow, Dr. Qihan Liu. Qihan completed his Ph.D. in Prof. Zhigang Suo’s lab here at Harvard University, where he focused on the mechanics and physics of soft materials.  Welcome, Qihan!