IOCBIO Sparks

IOCBIO Sparks is an open source software for detection of calcium sparks from confocal microscope line scan images. Sparks provides a user-friendly interface which was developed specifically for this task. All analysis results are stored in a database, either locally or using a central laboratory database. Such treatment of data allows researchers to analyze the measurements results using database tools and perform elaborate statistical analysis.

The software is developed in a cross-platform manner allowing to use it at different operating system platforms. For installation instructions, see README.

Links:

  • Project page: https://gitlab.com/iocbio/sparks.
  • Paper describing the software: Laasmaa, M., Karro, N., Birkedal, R., & Vendelin, M. (2019). IOCBIO Sparks detection and analysis software. PeerJ, 7, e6652 https://doi.org/10.7717/peerj.6652
  • Issues with the software and requests for help: https://gitlab.com/iocbio/sparks/issues. Please use the public issues when you want to get assistance with installation, reading your data, suggest extension or improvement of the software. By doing it openly, you can help others with the same problems or suggestions.
  • Example line scan recordings from mouse cardiomyocytes for testing the software:
    • in control solution, paced and later recorded at rest: data (20MB), background intensity is 10.5
    • in solution with isoprenaline, paced and later recorded at rest: data (18MB), background intensity is 10.1

Citation:

Please cite

if you use the software.

The software has been developed to make it extendable in terms of algorithms for sparks detection and background subtraction. We are open to add and test new approaches, consider analysis of image stacks for sparks detection, and extending application to detect similar events as sparks in other fields.