Data analysis Data analysis in [1] has been performed largely manual. In [2], the analysis has been revisited with DryMass [3] which enables an automated data analysis. The .cfg files are DryMass configuration files [4], i.e. analysis recipes that allow a complete data analysis from scratch. The file "HL60nuc.cfg" contains the basic data analysis recipe. The file "ignore_ROIs.txt" contains the ignored regions of interest for each measurement. The other .cfg files contain the same information with default values filled in by DryMass. The analysis has been tested with DryMass version 0.10.0.
To run an analysis, issue e.g. the following command:
References [1] M. Schürmann et al., "Cell nuclei have lower refractive index and mass density than cytoplasm," Journal of Biophotonics 9(10): 1068–1076, 2016. doi:10.1002/jbio.201500273. [2] P. Müller et al., "DryMass: handling and analyzing quantitative phase microscopy images of cell-sized objects," manuscript in preparation. [3] https://drymass.readthedocs.io/ [4] https://drymass.readthedocs.io/en/stable/sec_gs_configuration_file.html
Funding
European Union’s Seventh Framework Programme, Starting Grant "Light Touch" (282060)