Actin-crosslinking simulator
C co
de to simulate actin filament organization and energy storage with flexible crosslinkers
Please cite: Structural organization and energy storage in crosslinked actin assemblies. PLoS Computational Biology. 2018 May 29;14(5):e1006150. doi: 10.1371/journal.pcbi.1006150. PMID:29813051
Patch Tracking Tools
ImageJ plugins and macros for patch tracking and quality control for quantitative fluorescence microscopy.
Download the latest version of PatchTrackingTools (version 2015.12.16) with a documentation
(or clone the Bitbucket repository)
Download a sample movie and its analysis with PatchTrackingTools (~60 Mo)
If you have any issues or find glitches please contact Julien Berro (julien.berro@yale.edu)
Please cite: Local and global analysis of endocytic patch dynamics in fission yeast. Molecular Biology of the Cell. 2014 Nov 5;25(22):3501-14. PMID: 25143395
Older versions: PatchTrackingTools.2015.12.08.zip, PatchTrackingTools.2015.06.01.zip, PatchTrackingTools.2014.05.25.zip
Patch data post-processing tools
Matlab scripts to postprocess the data obtained with the PatchTrackingTools, including temporal super-resolution alignment (Berro and Pollard, 2014) and plotting functionalities.
PatchTrackingDataPostprocessing.160311.paper (Git).zip
(or clone the Bitbucket repository)
S. pombe Profiling Tools
ImageJ macros for cell profiling and montages for quantitative fluorescence microscopy.
Download (includes a documentation):
PombeProfilingTools.2012.12.09.zip
Please cite: Local and global analysis of endocytic patch dynamics in fission yeast. Molecular Biology of the Cell. 2014 Nov 5;25(22):3501-14. PMID: 25143395
Temporal Super-Resolution realignment
Simple Matlab demo of the temporal super-resolution realignment method:
DemoTemporalSuperResolution.zip
Please cite: Local and global analysis of endocytic patch dynamics in fission yeast. Molecular Biology of the Cell. 2014 Nov 5;25(22):3501-14. PMID: 25143395