Dense Flow reConstruction and Correlation (DFCC)

Reference to the publication: Haitham A Shaban, Roman Barth, Kerstin Bystricky; Formation of correlated chromatin domains at nanoscale dynamic resolution during transcription, Nucleic Acids Research, , gky269, https://doi.org/10.1093/nar/gky269

developed at:
Laboratoire de Biologie Moléculaire Eucaryote (LBME),
Centre de Biologie Intégrative (CBI), CNRS;
University of Toulouse, UPS; 31062
Toulouse; France

The software is provided "as is" as a set of MATLAB resource files and is tested under MATLAB version 7.5 (R2017b).

Required toolboxes:

• Image Processing Toolbox
• (optional) Optimization Toolbox

The script can be executed without the optimization toolbox. However, please be aware that uncertainties of fit parameters cannot be computed and are returned as NaN by the function 'AutocorrelationFit.m'.

Execute the file DFCC.m to process an example of a U2OS nucleus expressing H2B-GFP. The processed file can be easily changed by setting the appropriate directory (full path including filename and extension).

The example data takes ~1h 40 min on following system:

  Intel(R) Core(TM) i7-6700IQ CPU @ 2.60 GHz 2.60 Ghz     
  16.0 Gb RAM