This Matlab script allows quick batch analysis of Trackmate data with the MSD analyzer class.
The Read_Trackmate_xml_MSD_analyzer script is a batch processing focused tool to analyze large amounts of tracking data from the FIJI plugin Trackmate with the matlab class MSDanalyzer.
The Fast_large_Trackmate_xml_reader.m function is required for the Read_Trackmate_xml_MSD_analyzer script. It allows for quick loading of the xml files Trackmate creates.
Both Trackmate and MSDanalyzer are required to use this script.
Trackmate was developed by:
Jean-Yves Tinevez, Nick Perry, Johannes Schindelin, Genevieve M. Hoopes, Gregory D. Reynolds, Emmanuel Laplantine, Sebastian Y. Bednarek, Spencer L. Shorte, Kevin W. Eliceiri, TrackMate: An open and extensible platform for single-particle tracking, Methods, Available online 3 October 2016, ISSN 1046-2023, http://dx.doi.org/10.1016/j.ymeth.2016.09.016. (http://www.sciencedirect.com/science/article/pii/S1046202316303346)
And can be found here:
https://github.com/fiji/TrackMate
MSDanalyzer was developed by:
Nadine Tarantino, Jean-Yves Tinevez, Elizabeth Faris Crowell, Bertrand Boisson, Ricardo Henriques, Musa Mhlanga, Fabrice Agou, Alain Israël, and Emmanuel Laplantine. TNF and IL-1 exhibit distinct ubiquitin requirements for inducing NEMO-IKK supramolecular structures. J Cell Biol (2014) vol. 204 (2) pp. 231-45
And can be found here: