Given a 3-channel image (telomeres, cytoplasm, nuclei) the script segments the nuclei and the telomeres within the nuclei. The intensity of the segmented telomeres is then stored in an Excel spreadsheet along with the nuclear intensities and background intensities for both.
Dependencies
- Metamorph 7.7
- Microsoft Excel
Installation
Creating the Metamorph Taskbar
- Open Metamorph
- Under the Journal tab, choose Taskbars> Create Taskbar... to create a custom journal taskbar
- Within the Taskbar Editor navigate to where the two journals (downloaded from GitHub) are located. In the image below, the two journals are located in E:\WOLTERS\
- Highlight Load_Images.JNL and press Load to assign that journal as a button. Do the same for individual_cell.JNL.
- Save the journal taskbar by clicking Save As/Save.
Executing Taskbar
- Press the Load Images button: dialog box will appear requiring you to point to the directory where your images are located.
- Select the image with the appended c2 in the name. This script looks for the '_c#' where the # is 2, 3, or 4. You will need to change your image names to match this convention.
- The telomere image should be c2
- The cytoplasm should be c3
- The nuclei should be c4.
- See the example images (on GitHub).
- After a few seconds of processing, the telomere image will pop up with the segmented outline of nuclei overlayed.
- The journal is designed for the user to now select each segmented nuclear outline of interest using the left click on the mouse and then selecting the 'Individual _Cell' button.
- Upon the first selection an 'Open Data Log' window will pop up. Select 'OK.' This will cause an 'Export Log Data' window to open with Microsoft Excel selected in the application drop down menu. Change the sheet name as you see fit. Select OK.
- A Microsoft Excel spreadsheet will pop up populated with statistics from the current telomere selection.
- Continue selecting segmented regions until you're done.