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

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.

Congratulations to Stephanie Dauth, Ben Maoz, & Sean Sheehy on the cover of the Journal of Neurophysiology May 11th, 2017

Congratulations to our Brain Team for getting the cover of this month’s Journal of Neurophysiology “Neurons derived from different brain regions are inherently different in vitro: A novel multiregional brain-on-a-chip

Close-up image of axons that
have been grown over a 1-mm gap on a microcontact printed PLL/laminin lines connecting the different brain regions

Robotic Stingray wins Gold Medal at Edison Awards! April 25th, 2017

Congratulations to Professor Kit Parker and Sung-Jin Park, Ph.D. who received a gold medal in the engineering category at the Edison Awards for their work on the cyborg stingray.  The Edison Awards honor excellence in new product and service development, marketing, human-centered design and innovation.

 

Photo courtesy of Michael Rosnach

 

Welcome Dr. Cera and Dr. Lee! April 3rd, 2017

The DBG would like to extend a warm welcome to our new postdoctoral fellows, Luca Cera & Keel Yong Lee. Luca comes to us from Berlin, German, where he recently completed his Ph.D. in Chemistry under the guidance of Prof. Dr. Christoph A. Schalley. Keel Yong recently completed his Ph.D. in Prof. Kwanwoo Shin’s lab at Sogang University in Seoul, South Korea. We are looking forward to expanding on our past collaborations with him.

Congratulations to Karaghen Hudson, Leila Deravi & Nina Sinatra on the cover of Macromolecular Materials and Engineering! March 27th, 2017

Parker Lab Artist Karaghen Hudson’s illustration accompanying Leila Deravi & Nina Sinatra’s paper “Design and Fabrication of Fibrous Nanomaterials Using Pull Spinning” was chosen for the March 2017 cover of Macromolecular Materials and Engineering.

 

 

Pull spinning is a new nanofiber manufacturing technique that uses a high-speed rotating bristle to draw anisotropic nanofibers from a polymer solution. The versatile structure and composition of scaffolds formed using pull spinning enables a wide range of applications, including muscle tissue engineering and textile design.