Quantitative data of key-event dynamics extracted from images of time-lapse microscopy from Infinite invitro assessment of lung inflammation within nanoPASS

The repository contains quantitative data of key-event dynamics extracted from images of time-lapse microscopy over 1–2 days, for benchmark and industrial materials on in vitro models for selected adverse outcomes. For each material, the data consists of example microscopy images (three time-points, all channles, all conditions, one biological replicate) and tables with quantification data for whole time-series for each condition.

The data in the folders is structured as follows (also in readme.txt):

Parent directory includes

• directories with data for per material. Name (or in some cases code) of the material is directory name
      material_services_map.json - includes a a map between materials and experiment names

Each directory for material consists of

• Here microscopy metadata excel file acquisition_matadata_pretty.xlsx.
• Directories named [experiment_code] - directories of experiments. It includes
  • quantification_data subdirectory with quantification results in form of excel spread sheet for each biological replicate and each condition. The structure of quantification file names: 
    • [experiment_code]-[well_id]_report_[condition].xlsx
      • [experiment_code]: code of an experiment, this material was analyzed in, usually INFXXX format
      • [well_id]: number differs between materials in different wells
      • [condition]: marks the type of cells used in the experiments (epi - epitehlial cells, imu - imune cells, epiimu - co-culture of both)
  • image directory containg example of .tif images used for quantification that results in excel spreadsheet. Each contains a set of images from individual mult-channel multi-position time-lapse experiment with different cell combinations exposed to nanomaterial stated in parent directory name. Microscopy metadata for this experiment is included in a subfolder with matching [experiment_code] id from the file name. The filename structure:
    • IMGxxx_[experiment_code]-[well_id]_tile[tile_number]_[channel]_[cell_type]_t[time_point].tif
      • [experiment_code]: code of an experiment, this material was analyzed in, usually INFXXX format
      • [well_id]: number differs between materials in different wells
      • [tile_number]: two xy-tiles per condition
      • [channel]: cytoplasm of epi cells (LA4), membrane (MEM), cytoplasm of imu cells and tubulin (MHSTUB), nanomaterial (NANO)
      • [cell_type]: mono-culture of lung epithelial cells (epi), mono-culture of macrophages (imu) or their coculture with macrophages (epiimu) 

The data acquistion and analysis were co-funded by private RnD funds by Infinite d.o.o.