IOCBIO Sparks is open-source software for detecting calcium sparks in confocal microscope line-scan images. Sparks provides a user-friendly interface developed specifically for this task. All analysis results are stored in a database, either locally or using a central laboratory database. This treatment of data allows researchers to analyze measurement results using database tools and perform elaborate statistical analysis.
The software is developed to run on different operating systems. For installation instructions, see the README.
Links
- Homepage: https://iocbio.gitlab.io/sparks/
- Project page: https://gitlab.com/iocbio/sparks.
- Demo video: https://www.youtube.com/watch?v=8xWKB--RNn4
- Issues with the software and requests for help: https://gitlab.com/iocbio/sparks/-/work_items. Please use the public issues when you want assistance with installation, reading your data, or suggesting an extension or improvement to the software. By doing so 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
- 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
if you use the software.
The software has been developed to make it extensible in terms of algorithms for spark detection and background subtraction. We are open to adding and testing new approaches, considering the analysis of image stacks for spark detection, and extending the application to detect similar events in other fields.