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Digital holograms of isolated HL60 cell nuclei

dataset
posted on 05.11.2019, 21:38 by Mirjam Schürmann, Jana Scholze, Paul Müller, Jochen Guck, Chii J. Chan
Digital holograms of isolated HL60 cell nuclei

These data were originally used by Schürmann et al. [1] for the
quantification of the refractive index of isolated HL60 cell nuclei.


Raw data
The data are related to [1] according to the following scheme
(last part before suffix indicates cell cycle stage):

Figure 5 - 1st measurement:
2014-05-29_DHM_HL60-nuclei-G1.zip
2014-05-29_DHM_HL60-nuclei-G2.zip
2014-05-29_DHM_HL60-nuclei-S.zip

Figure 5 - 2nd measurement:
2014-07-03_DHM_HL60-nuclei-G1.zip
2014-07-03_DHM_HL60-nuclei-G2.zip
2014-07-03_DHM_HL60-nuclei-S.zip


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:

dm_analyze_sphere -p 2014-05-29_DHM_HL60-nuclei-G1.cfg 2014-05-29_DHM_HL60-nuclei-G1.zip


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)

Alexander-von-Humboldt Stiftung, Humboldt-Professorship

European Communitys Seventh Framework Programme (FP7/2007-2013) grant 264399 (ITN "TRANSPOL")

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