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.

What's New

Picture of the Month – April 2012 April 6th, 2012

Isotropic cardiac myocyte monolayer stained for actin (red), beta-catenin (white), and nuclear DNA (blue). Image by Megan McCain, Parker lab.

Congrats to Kartik Balachandran! March 14th, 2012

Kartik Balachandran has been awarded the Postdoctoral Fellow Best Abstract Award by the Association of Scientists of Indian Origin Special Interest Group of the Society of Toxicology (SOT) at the SOT Annual Meeting in San Francisco, CA. This competitive award was based on a submitted abstract and a cover letter outlining the significance of his research. The award includes a plaque and monetary award of $500. Congratulations, Kartik!!

Congrats to Josh Goss!! March 5th, 2012

Josh Goss is one of the winners of the first Harvard School of Engineering and Applied Sciences Dean’s Excellence Award. Josh is the senior instrumentation engineer and staff scientists in the Disease Biophysics Group, designing and prototyping all of our experimental systems from microfluidic systems for organs on chips to blast bioreactors for brain injury research. Congratulations, Josh!! Thanks for all of your hard work!!

Picture of the Month – February 2012 February 24th, 2012

Micropatterned mouse ventricular muscle cells assembled into an anisotropic tissue showing nuclei (pink) and organized sarcomeres (orange). This organization recapitulates features of the native architecture of cardiac tissue. Image by Anna Grosberg, Parker lab.

Postdoctoral Positions in the DBG February 19th, 2012

We have several postdoctoral positions opening now and in the coming months. We are especially interested in candidates with backgrounds in theoretical biomechanics who are interested in conducting bench experiments. These positions will focus on our efforts to recapitulate organ-level function on chips for drug discovery and safety pharmacology.

All of these positions require a doctoral degree in an appropriate field and a demonstrated publication record. Applications in the form of a single PDF file containing a cover letter, resume, and up to three examples of first author papers should be forwarded to Prof Parker (kkparker@seas.harvard.edu). A list of references should be submitted with the resume with contact information.