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

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!

Farewell Jack! June 16th, 2017

The DBG would like to wish Jack Zhou all the best as he leaves us for his next adventure – Medical School. Congratulations Jack!

The DBG welcomes the Orientation and Reach-Back Training class of the U.S. Army May 22nd, 2017

The DBG had the pleasure of hosting the Orientation and Reach-Back Training (ORBT) training class of the U.S. Army Research, Development and Engineering Command (RDECOM) Field Assistance in Science and Technology (FAST) program on May 17, 2017. ORBT is a multi-week mission overview program for senior-level Army officers, non-commissioned officers and Department of the Army civilians on the mechanisms for identifying and resolving technology capability gaps for units in their area of operation. The class visit to Professor (Lieutenant Colonel, Reserves) Parker’s Lab is their only visit to a Lab outside the Department of Defense.

The class met with DBG veterans and attended presentations on Stronger, Tougher, and Lighter Soldier Protection Systems; Nanofiber Scaffolds for Wound Healing/Dressings; Traumatic Brain Injury – Understanding Disease Mechanisms; Fibrous Scaffolds for Tissue Engineered Foods; Cells as Engineering Materials – the Cyborg Ray Project; Cuttlefish Inspired Camouflage; and our unique program for embedding Artists-In- Residence in the Lab.

Guests included members from the U.S. Army Research, Development, and Engineering Command (RDECOM); U.S. Army Engineer Research and Development Center (ERDC); U.S. Army Corps of Engineers; Army Research Laboratory; and RDECOM Research, Development and Engineering Centers.

Pictured below are (clockwise from bottom left): DBG Artist-in- Residence Karaghen Hudson (Harvard Class of 2018); Ms. Valerie Carney (ERDC); Dr. Aimee Poda (ERDC); Dr. (Colonel, Reserves) Steve Hart (RDECOM); Veteran and Program Coordinator John Laursen (Army Retired); Dr. Jerry Ballard (ERDC); Mr. Nathan Frantz (US Army Corps of Engineers); Visiting Scholar and Brigadier General Michael D. Phillips (USA Retired); Dr. Samantha Chambers RDECOM Science Advisor to the XVIII Airborne Corps; and Lieutenant Colonel Jovanna Nelson.