Supplementary_File_1c_Spreadsheet_Instructions_Waters_S_160122646

Supplementary file 1a contains a dedicated spreadsheet designed to semi-automate the process of measuring vacancy-type defects
from TEM micrographs using the “Intensity Profile” and “Multi Plot” tools incorporated into the software package ImageJ.

Supplementary file 1b contains an example dataset to be used with this spreadsheet.

Instructions / additional explanation:

1. Open Supplementary file 1b, copy all of the data in the sheet to the clipboard.

2. Open Supplementary file 1a, paste the data into cell A1 in sheet 1.

3. An an automated series of sheets (sheets 2-4) pre-processes the data according to the procedure detailed in Chapter 3 (3.3.5)
   *There is no need to edit these sheets in any way

4. Graphical outputs of linescans obtained from Over- and Under-focussed micrographs are displayed automatically in Sheets 5 and 6 respectively. (Rows 57-106)

5. Cell C109 contains a field which will automatically update the chosen threshold intensity (%) at which the horizontal (black) line crosses the data (blue)
   Amending the number in cell C109 will result in automated update of graphical outputs (horizontal line (black) and vertical intersects(red)) 
   and the corresponding numerical outputs (generated in row 130).  
   *Note that the horizontal (black) line must intersect the data (blue) twice to work correctly, an error is generated in the corresponding numerical output 
    cell if this is not the case.

6. Mean average defect sizes of individual defects are output to column F of Sheet 7. (calculated according to the procedure detailed in Chapter 3 (3.3.5))
   The mean average defect size cresponding to the entire dataset are output in cell F54 of Sheet 7. Corresponding errors are output to cells F55 and F56.

7. Histograms of defect size distributions are constructed automatically in columns Q to Z of sheet 7.
   The number of categories (bins) into which the population is distributed can be altered by changing the value in cell J2 of sheet 7.
   The corresponding histogram is updated automatically according to the value input into J2

8. Sheets 8 and 9 (obselete) contains data obtained from Over- and Under-focus micrographs which has not been averaged.