Software

Actin-crosslinking simulator

C code to simulate actin filament organization and energy storage with flexible crosslinkers

Download from Bitbucket

Please cite: Ma R and Berro J. 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:

Berro J and Pollard TD. 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

Lemière J, Ren Y, Berro J. 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:

Berro J and Pollard TD. 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

Lemière J, Ren Y, Berro J. 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: Berro J and Pollard TD. 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: Berro J and Pollard TD. 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