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

DBG Lab is Operational! March 15th, 2021

After 17 years of outstanding science in Cambridge, the DBG has moved to the Engineering School’s new campus in Allston. As of March 2, the lab is fully operational and has resumed experiments. Thank you to all alumni and current personnel for constantly raising the bar. Stand by for the next chapter of DBG science!

Congratulations to Dr. Megan McCain! March 10th, 2021

Our congratulations go out to DBG alumna, Dr. Megan McCain, who has recently received tenure at University of Southern California!

Farewell to Dr. Suhwan Kim! January 13th, 2021

Congratulations to Dr. Suhwan Kim, who has accepted a position as an Assistant Professor in the Department of Chemical Engineering at Dong-A University in Basun, South Korea! Dr. Kim was an integral part of our brain team for over a year as a postdoctoral fellow. We wish him the best on this next step in his career!

Inaugural Issue — Biophysics Reviews! January 4th, 2021

Dr. Kevin Kit Parker launched Biophysics Reviews, a new peer-reviewed journal for the biophysics research community on December 14. Produced by scientific publisher AIP Publishing, the aims to expand “on the tradition of excellence set by Applied Physics Reviews (APR) by publishing high impact, cutting edge research and reviews that are valuable for both emerging and experienced researchers”.

References:
1. KK Parker, L Longobardi, A Sulicz. “Welcome to Biophysics Reviews, a big tent for the biophysics community”. Biophysics Reviews. 14 Dec 2020; 1(1); 010401. https://doi.org/10.1063/5.0036408.

A Belated Farewell and Congratulations to Dr. Ardoña! October 14th, 2020

Congratulations to Dr. Herdeline Ardoña, who has accepted a position as an Assistant Professor in the University of California Irvine Department of Chemical and Biomolecular Engineering. She joined the Disease Biophysics Group as a postdoctoral fellow in 2017 and was an essential part of our research and mentoring team. Best of luck to you as you settle in and get your research group up and running!