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

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!

Congratulations to our new Ph.D.’s! June 7th, 2019

Congratulations to our newest PhD recipients Grant Gonzalez and Seungkuk Ahn! We thank them for their excellent achievements, and are looking forward to seeing their future work.

The Stingray goes to Paris! March 26th, 2019

The Disease Biophysics Group is at the Pompidou Centre! The centre’s Designing the Living exhibit is part of the Mutations/Créations 3 program. It includes our soft-robotic ray, featured on the cover of Science (Vol 353, Issue 6295; 08 July 2016). The exhibit showcases the interplay of bioengineering with art, and was curated by Marie-Ange Brayer and Olivier Zeitoun. A video of the exhibit can be found on the Pompidou Centre program page.

2019 DBG Retreat January 17th, 2019

The Disease Biophysics Group just returned from its annual retreat! For two days, DBGers presented research updates to the group and our visiting collaborators.

2018 HIRN Meeting at Harvard January 12th, 2019

In December 2018 we hosted the Human Islet Research Network’s (HIRN) NIH investigator meeting. Professor Parker treated the visitors to BBQ brisket and chicken as they discussed the state of the field and toured through DBG labs for numerous demonstrations.