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ImageJ GT Steps.md

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ImageJ Steps

This was the process used to generate the masks and the regions of interest (ROIs) from the SEM images using ImageJ.

Creating new masks and ROIs

Add all the holes as ROIs

  1. File > Open the desired image.
  2. Analyze > Tools > ROI Manager... to open the ROI manager tool.
  3. Using the ellipse (or other) selection tool from the toolbar, draw a ROI around the desired hole.
  4. Click Add [t] in the ROI manager to add your selection to the ROI list.
  5. Repeat steps 3 & 4 for each hole.

Save the ROIs

  1. Once all the desired ROIs are in the ROI list, make sure none of them are highlighted by clicking deselect in the ROI manager.
  2. Click More > Save... in the ROI manager and save your ROIs. It should try to save a .zip file containing the .roi ROI file for each selection. If it's saving a .roi file, likely one of the ROIs is highlighted.

Create a binary mask from the ROIs

  1. With all the ROIs in the ROI list, highlight all of them by CTRL+Click or CTRL+A.
  2. Right-click the selection and OR (Combine) the ROIs.
  3. Edit > Selection > Create Mask to open a new window with the created binary mask.
  4. With the binary image in focue, File > Save As and select a desired file type to save in. Usually TIFF files are appropriate.

Create formatted CSV of hole dimensions

  1. Open the detailed list of ROIs in the ROI manager using More > List.
  2. Save the detailed list using File > Save As... in new window that popped up to save a preliminary CSV file.
  3. In the terminal, navigate to the folder where you saved the CSV and run python format_roi_csv.py [filename.csv] to format the data. Add the arguments -s [x, y] to sort in a direction or -m [metadata.txt] to read metadata from another file.

Editing existing ROIs

Update ROIs

  1. File > Open the desired image.
  2. In the ROI Manager, More > Open... the ROI zip file.
  3. To edit an existing ROI, highlight it in the ROI manager. Then, adjust your selection as desired. Once finished, click Update in the ROI manager. Save in the same way as before.