We distribute our software via GitHub: https://github.com/kjaqaman. Below we describe the different software packages, with links to their associated papers and individual GitHub locations.
*** u-track (multiple-particle tracking)
Multiple-particle tracking software designed to:

- Track dense particle fields.
- Close gaps in particle trajectories resulting from detection failure.
- Capture particle merging and splitting events resulting from occlusion or genuine aggregation and dissociation events.
Its core is based on formulating correspondence problems as linear assignment problems and searching for a globally optimal solution. The software can be called either via a Graphical User Interface or command line.
For more information, please see Jaqaman et al., Nature Methods 5, pp. 695-702 (2008).
- Software on GitHub - download
*** Diffusion mode analysis from frame-to-frame displacements
Diffusion analysis software designed to:
- Calculate the diffusion coefficient of a particle track from its frame-to-frame displacements.
- Categorize each particle track into a diffusion mode based on its diffusion coefficient (diffusion modes identified either manually or via analysis of the frame-to-frame displacement distribution).
For more information, please see Jaqaman et al., Molecular Biology of the Cell 27, pp. 1561-1569 (2016).
- Software on GitHub - download
*** ColocP2C (colocalization analysis)
Colocalization analysis software designed to:
- Assess colocalization between two molecular entities from multi-channel high-resolution light microscopy images when one molecule has a punctate appearance while the other has a continuous appearance.
- Assess the above colocalization in the context of a third molecular entity (i.e. "conditional" colocalization).
For more information, please see Maringa-Githaka et al., Journal of Cell Science 129, pp. 4175-4189 (2016).
- Software on GitHub - download
*** DC-MSS (transient motion analysis)
Transient motion analysis software designed to:
- Distinguish between free diffusion, confined diffusion, immobility and diffusion with drift.
- Segment tracks into subparts exhibiting the different motion classes.
For more information, please see Vega et al., Biophysical Journal 114, pp. 1018-1025 (2018).
- Software on GitHub - download
*** FISIK (derivation of molecular interaction kinetics)
Framework for the Inference of in Situ Interaction Kinetics from single-molecule tracking data with sub-stoichiometric labeling. It consists of two components:
- A stochastic mathematical model of molecular movement and interactions, mimicking the biological system and data acquisition setup, including sub-stoichiometric labeling.
- Model Calibration with experimental single-molecule data to estimate molecular association and dissociation rates.
The supplied software implements the framework for a simple model of freely diffusing molecules in 2D. For more information, please see de Oliveira and Jaqaman, Biophysical Journal 117, pp. 1012-1028 (2019).
- Software on GitHub - download
*** Detection of network-like biological structures
Software for the detection of lines and their intersections in network-like biological structures in light microscopy images, such as cytoskeletal filaments and meshworks or stained membranes in a cell sheet. Its key features include:
- Analytial derivation of multi-orientation information per pixel after curvilinear feature (i.e. ridge) filtering.
- Use of multi-orientation information from filters with different spatial localizations in order to balance orientation resolution and spatial localization.
- Parsimonious segmentation of lines and their intersections of arbitrary geometry.
For more information, please see Kittisopikul et al., Bioinformatics, Online ahead of print (2020).
- Software on GitHub - download