Advanced sCMOS camera technology has recently enabled dramatic increases in the number of single molecules that can be imaged simultaneously at high speeds, while achieving equal or better data quality compared to state of the art EMCCDs. To rapidly analyze recordings from tens of thousands of molecules, we developed SPARTAN, a suite of tools for extracting traces from movies, selecting traces according to defined criteria, applying corrections, hidden Markov modeling, simulation, and data visualization. These tools are largely automated, requiring only minimal user input and time to proceed from raw data to interpretable results. The MATLAB source code also provides a rich platform for developing new analysis tools.
If you use the software or algorithms for your data analysis, please cite the following paper:
Juette, M. F., Terry, D. S., Wasserman, M. R., Altman, R. B., Zhou, Z., Zhao, H. & Blanchard, S. C. Single-molecule imaging of non-equilibrium molecular ensembles on the millisecond scale. Nature Methods 13, p. 341 (2016).
This program was developed at Cornell University and St Jude Children's Research Hospital with direct contributions from the following people (listed in alphabetical order):
- Peter Geggier
- Manuel F. Juette
- Zeliha Kilic
- Roman Kiselev
- James B. Munro
- Daniel S. Terry (primary author)
SPARTAN also contains code from third-party projects (listed in alphabetical order):
- Bob Hamans: https://www.mathworks.com/matlabcentral/fileexchange/16216-regexpdir
- Tim Holy: https://www.mathworks.com/matlabcentral/fileexchange/29702-generate-maximally-perceptually-distinct-colors
- Igore Kaufman: http://www.mathworks.com/matlabcentral/fileexchange/34054-merge-structures/
This software collects optional telemetry that is used for aggregate usage statistics to help us maintain funding and support. Any information collected is used solely for research and software-improvement purposes. It will not be sold or disclosed to third parties.
When telemetry is enabled, the following anonymous data are collected:
- Basic usage events like software start.
- Application version
- Operating system and platform
- Approximate geographic region (derived from IP address)
Telemetry data are sent to PostHog, a hosted analytics service, and are
retained for a period of one year. You can disable telemetry at any time
by executing the following command on the MATLAB console:
setpref('SPARTAN', 'out_out', false);