Table 1 Overview of data files
Label | Name of data file/data set | File types (file extension) | Data repository and identifier (DOI or accession number) |
|---|---|---|---|
DAPI channel, 365Â nm excitation wavelength, 16 bit pixel depth confocal fluorescence microscopic images, stacks of 96 well plates (7 files) | Image stacks saved in LZW compressed, native ImageJ .zip format that can be opened with ImageJ after renaming the extension from .zip_ to .zip | Harvard Dataverse [10] | |
ER tracker channel, 488Â nm laser excitation wavelength, 16 bit pixel depth confocal fluorescence microscopic images, stacks of 96 well plates (7 files) | Image stacks saved in LZW compressed, native ImageJ .zip format that can be opened with ImageJ after renaming the extension from .zip_ to .zip | Harvard Dataverse https://0-doi-org.brum.beds.ac.uk/10.7910/DVN/FYGHFO | |
mCherry Salmonella channel, 561Â nm laser excitation wavelength, 16 bit pixel depth confocal fluorescence microscopic images, stacks of 96 well plates (7 files) | Image stacks saved in LZW compressed, native ImageJ .zip format that can be opened with ImageJ after renaming the extension from .zip_ to .zip | Harvard Dataverse https://doi.org/10.7910/DVN/FYGHFO | |
ST_exp60_confocal_infection_plates.xls | Plate layout including ERT concentrations | MS Excel file (.xls) | Harvard Dataverse https://0-doi-org.brum.beds.ac.uk/10.7910/DVN/FYGHFO |
Plate 2_Thr = 235.tif.zip_ | Segmented 8 bit pixel depth binary images, stacks of 96 well plates | Image stacks saved in LZW compressed, native ImageJ .zip format that can be opened with ImageJ after renaming the extension from .zip_ to .zip | Harvard Dataverse https://0-doi-org.brum.beds.ac.uk/10.7910/DVN/FYGHFO |
Plate 3_Thr = 180.tif.zip_ | Same as above | Same as above | Same as above |
Plate 4_Thr228-7275.tif.zip_ | Same as above | Same as above | Same as above |
Plate 5_Thr = 270.tif.zip_ | Same as above | Same as above | Same as above |
Plate 6_Thr = 197_sizefiltered_250px- = 26um2-.tif.zip_ | Same as above | Same as above | Same as above |
Plate 7_Thr = 177_sizefiltered_250px- = 26um2-.tif.zip_ | Same as above | Same as above | Same as above |
ImageJ_macro_ijm.txt | ImageJ macro file | Text file (.txt) | Harvard Dataverse https://0-doi-org.brum.beds.ac.uk/10.7910/DVN/FYGHFO |
Infected_cell_ER_signal_Plate 2–7.zip_ | Table containing extracted features as a result of image analysis | LZW compressed (.zip) Comma Separated Value (.csv) text files that can be opened for further processing with R or MS Excel after renaming the extension from .zip_ to .zip and uncompress | Harvard Dataverse https://0-doi-org.brum.beds.ac.uk/10.7910/DVN/FYGHFO |
Plates 2–3.R | R script | Text file (.txt) | Harvard Dataverse https://0-doi-org.brum.beds.ac.uk/10.7910/DVN/FYGHFO |
Plates 4–5.R | R script | Text file (.txt) | Harvard Dataverse https://0-doi-org.brum.beds.ac.uk/10.7910/DVN/FYGHFO |
Plates 6–7.R | R script | Text file (.txt) | Harvard Dataverse https://0-doi-org.brum.beds.ac.uk/10.7910/DVN/FYGHFO |