####Dataset Description#### These datasets have been made available so that interested parties can examine the effects of miscounting from multiple points in the workflow. The verticies represent the 200 cell geometry examples used, meaning geomID=1 is cell geometry 1 in all subsequent datasets. SDDs are the DNA damage simulation output files carried out on the verticies as described in Ingram, s., et al. [1]. Each combination of damage and geometry file then has a representitive microscope file emulated (DSB Marker and H2AX Marker). The Repair - * zip files are the positions of the flourescent objects as a function of time for PyFoci to then emulate a microscopic image from. ####Vertices.zip#### This data describes the Hi-C geomtry files for IMR90 cells. These descriptions are used to define topologically-associated domains used in the histone modelling. For more details on how these files are created see Ingram, s., et al. [1] ####SDDs.zip#### This data is provided as the comprehensive version of the Standard DNA Damage (SDD) format, which is standardised format for storing DNA damage data. Filename is given as {energy}_{dose}_{particle}_{geomID}.sdd. Note that all photon SDD files are for cobalt-60 simulation. Exact details of the format should can be found in the paper by Schuemann, J., et al.[2] There is a SDD parser included within the PyFoci project. ####Repair - DSBMarker.zip#### This is the data which describes the DSB distribution for PyFoci as a function of time. Folder structure is {particle}/{energy}/{dose} and the files are called MicroscopeSnapshots{geomID}.out These are simple text files which are space seperated where each line is a DNA end. The columns are: time, x, y, z, intensity, het/eu, chromosomeID, chromatidID, long/short Arm, PositionAlongChromosome (0-1) Each line is a DSB end (i.e. 2 per DSB). ####Repair - H2AXMarker_{particle}_{dose}.zip#### This is the data which describes the histone activation caused from the DSB distribution for PyFoci as a function of time. Files are stored in seperate zips due to the large file size. Files are stored as compressed binary files .npz which can be read by Python's numpy. PyFoci can read the files directly and make the corresponding images as required. Filename MicroscopeSnapshotH2AX_{geomID}.npz details which geometry the simulation is of. The corresponding MicroscopeSnapshots{geomID}.out where you match particle, energy, dose will be the matching DSB marker distribution (i.e. based on the same DSB distribution and repair). ####FociCountedDatasets.zip#### This is the processed datasets for how many foci where detected in for each microscope generated image (single z-slice through the cell center). Each dataset is for a specific microscope-magnification combination. The files are .parquet files which can be read in using Python Pandas module. This will present the details of all analysed files within and the results. ####References#### [1] Ingram, S. P. et al. Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage. Plos Comput Biol 16, e1008476 (2020). [2] Schuemann, J., McNamara, A., Warmenhoven, J., Henthorn, N., Kirkby, K., Merchant, M., Ingram, S., Paganetti, H., Held, K., Ramos-Mendez, J., Faddegon, B., Perl, J., Goodhead, D., Plante, I., Rabus, H., Nettelbeck, H., Friedland, W., Kundrát, P., Ottolenghi, A., Baiocco, G., Barbieri, S., Dingfelder, M., Incerti, S., Villagrasa, C., Bueno, M., Bernal, M., Guatelli, S., Sakata, D., Brown, J., Francis, Z., Kyriakou, I., Lampe, N., Ballarini, F., Carante, M., Davídková, M., Štěpán, V., Jia, X., Cucinotta, F., Schulte, R., Stewart, R., Carlson, D., Galer, S., Kuncic, Z., Lacombe, S., Milligan, J., Cho, S., Sawakuchi, G., Inaniwa, T., Sato, T., Li, W., Solov'yov, A., Surdutovich, E., Durante, M., Prise, K., McMahon, S. (2018). A New Standard DNA Damage (SDD) Data Format Radiation Research https://dx.doi.org/10.1667/rr15209.1