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.

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What's New

2019 MRS Conference Award Winners December 10th, 2019

Congratulations to Dr. Luke MacQueen and Dr. John Zimmerman for the Best Poster and Best Poster Nominee awards at the 2019 MRS in Boston!

Luke MacQueen
John Zimmerman

DBG Alumni Awarded ERC Starting Grant November 12th, 2019

Congratulations to DBG alumni Francesco Pasqualini (University of Pavia, Italy) and Ben Maoz (Tel Aviv University, Israel), and longtime associate Maximilian Emmert (Universität Zürich, Switzerland), for being awarded the prestigious ERC Starting Grant this year!

Farewell Seungkuk! September 5th, 2019

Congratulations to Dr. Seungkuk Ahn, who has accepted a position as a Postdoctoral Fellow in the Biophysics Group in ETH Zürich with Professor Daniel J. Müller. Seungkuk joined the Disease Biophysics Group as a graduate student in 2012, and departed for Switzerland this past month. Congratulations Seungkuk!

Thank you to our 2019 summer students! September 5th, 2019

Thank you to the undergraduate students who visited our lab this summer. We wish you all the best in your future endeavors!
 

Riley Flores
Rudy Gabardi
James Ikeda
Christina Pizza
Danielle Gamboa
Carlos Marquez

Welcome 2019 Summer Students! June 17th, 2019

The Disease Biophysics Group welcomes our 2019 summer students! From left to right: Rudy Gabardi, Carlos Marquez, James Ikeda, Christina Pizza, Danielle Gamboa, and Riley Flores. Best of luck on your summer research projects!