Biological and Physical Sciences (BPS) Microscopy Benchmark Training Dataset Documentation:
Authors: Lauren M. Sanders, NASA Open Science Data Repository
Pending NASA Software Release, dataset generation code will be available on GitHub and this document will be updated with the link.
Data Organization:
nasa-bps-training-data bucket:
/Microscopy
/train (directory containing FITC 53bp1 stained images)
meta.csv (within the /train directory: metadata file for all FITC images with dose in units of Gray, particle type, and hours after radiation exposure image was taken)
/DAPI_MASK_images (directory containing the DAPI and MASK images)
meta_DAPI_MASK.csv (metadata file for all DAPI and MASK images with dose in units of Gray, particle type, and hours after radiation exposure image was taken)
Data Origin:
- The original data for this benchmark dataset are fluorescence microscopy images of individual nuclei from mouse fibroblast cells, irradiated with Fe particles or X-rays with fluorescent foci indicating 53BP1 positivity, a marker of DNA damage(Penninckx et al. 2019).
- Additional information and data are available on the NASA Open Science Data Repository: OSD-366 (DOI: 10.26030/v8w4-rg83)
- Images from the following plates are included in this dataset:
P278
P279
P280
P282
P283
P284
P286
P287
P288
P242
P243
P244
P248
P249
P250
P251
P253
- Each plate contained 96 wells (see image below for a 96-well plate). Each well was coated with cells from a specific mouse and imaged at a specific time, and each plate underwent a specific radiation exposure.
Data Preprocessing:
- Starting from the 9-layer microscopy Z-stack .ics images, the Python library diplib was used to generate maximum intensity projection images.
References
Penninckx, Sébastien, Egle Cekanaviciute, Charlotte Degorre, Elodie Guiet, Louise Viger, Stéphane Lucas, and Sylvain V. Costes. 2019. “Dose, LET and Strain Dependence of Radiation-Induced 53BP1 Foci in 15 Mouse Strains Ex Vivo Introducing Novel DNA Damage Metrics.” Radiation Research 192 (1): 1–12.