GitHub - romanbarth/Hi-D: MATLAB files for the Hi-D approach presented in Shaban, H.; Barth, R.; Recoules, L.; Bystricky, K.; Hi-D: Nanoscale mapping of nuclear dynamics in single living cells. Genome Biology (2020). Released under the GNU General Public License.

romanbarth / Hi-D Public

MATLAB files for the Hi-D approach presented in Shaban, H.; Barth, R.; Recoules, L.; Bystricky, K.; Hi-D: Nanoscale mapping of nuclear dynamics in single living cells. Genome Biology (2020). Released under the GNU General Public License.

GPL-3.0 license

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Name		Name	Last commit message	Last commit date
Latest commit History 17 Commits
3rdParty		3rdParty
Code		Code
HiD.m		HiD.m
LICENSE		LICENSE
U2OS_DNA_Serum_example_data.tif		U2OS_DNA_Serum_example_data.tif
initialize.m		initialize.m
license_3rd_party.txt		license_3rd_party.txt
readme.txt		readme.txt

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 HiD
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Shaban, H.; Barth, R.; Recoules, L.; Bystricky, K.; Hi-D: Nanoscale mapping of nuclear dynamics in single living cells. Genome Biology (2020)

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The software is provided "as is" under the GNU General Public License as a set of MATLAB resource files and is 
tested under MATLAB version 7.5 (R2017b).
If you use this code or parts of it in your research, please refer to our publication.

Required toolboxes:

- Image Processing Toolbox
- Optimization Toolbox (for Bayesian model selection)
- Statistics Toolbox (for Bayesian model selection)

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

The example data takes ~2h 20 min on following system:
      Intel(R) Core(TM) i7-6700IQ CPU @ 2.60 GHz 2.60 Ghz
      16.0 Gb RAM