Data · dataset · 2019
Digital holograms of isolated HL60 cell nuclei
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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.
Description
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.
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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] drymass.readthedocs.io/ [4] drymass.readthedocs.io/en/stable/sec_gs_configuration_file.html
Links
Where it is published
- Repository landing page figshare.com/articles/Digital_holograms_of_isolated_HL60_cell_nuclei/102574… ↗
landing page · from DataCite
- DOI doi.org/10.6084/m9.figshare.10257458.v1 ↗
DOI / persistent id · from DataCite
Documentation and papers
- Creative Commons Zero v1.0 Universal creativecommons.org/publicdomain/zero/1.0/legalcode ↗
license · from DataCite
Catalogue records · 2
- DataCite API api.datacite.org/dois/10.6084/m9.figshare.10257458.v1 ↗
metadata API · from DataCite
- DataCite Commons commons.datacite.org/doi.org/10.6084/m9.figshare.10257458.v1 ↗
catalogue entry · from DataCite
Topics
- Stated by source
- Basic medicine
- Inferred from text
- Image 65% · Microscopy 75%
Related
Provenance · 1 source records, 11 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| DataCite | 10.6084/m9.figshare.10257458.v1 | 14 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| byte_size | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].fos:basic-medicine | source · DataCite | connector:datacite@1.0.0 | |
| concepts[modality].local:modality:image | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:microscopy | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · DataCite | connector:datacite@1.0.0 | |
| description | source · DataCite | connector:datacite@1.0.0 | /data/attributes/descriptions |
| license | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| publication_date | source · DataCite | connector:datacite@1.0.0 | /data/attributes/dates |
| title | source · DataCite | connector:datacite@1.0.0 | /data/attributes/titles/0/title |
| updated_date | source · DataCite | connector:datacite@1.0.0 |