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
and
. Adaptation of actin dynamics and membrane tension control for yeast endocytosis.BioRxiv 342030 [Preprint]. November 23, 2020.
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.
Download PatchTrackingDataPostprocessing.160311.Deterministic.210128.zip
(or clone the Bitbucket repository)
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
and
. Adaptation of actin dynamics and membrane tension control for yeast endocytosis.BioRxiv 342030 [Preprint]. November 23, 2020.
Older version: PatchTrackingDataPostprocessing.160311.paper (Git).zip
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