TITLE: Movie_Timepoint_CopytoClipboard_Tool
AUTHORS: Condon  ND

[DESCRIPTION]
This protocol describes how to use the Movie-Timepoint_CopytoClipboard_Tool.ijm program made by Nicholas Condon at the Institute for Molecular Bioscience's Microscopy core facility at The University of Queensland, Brisbane, Australia.

This tool allows the user to quickly generate figures in programs external to FIJI for time-series data. It allows the user to choose which channels of the open image they would like incorporated, as well as an optional Merged panel. Users then navigate to each frame and a series of popups will guide them through pasting the image frames into their program of choice. This tool records the frame numbers chosen and the corresponding time value (if known from the image metadata file). There is also the option to save out the results into a user-chosen directory for better record keeping. A log with the frame number and timepoint information is also saved.

[STEPS]
SECTION: Running the Script
1. Launch FIJI

  

SECTION: Running the Script
2. Open your time-series dataset into FIJI
  

SECTION: Running the Script
3. Open the Movie Timepoint CopytoClipboard Tool script
[Plugins > Macros > Run...
   

SECTION: Running the Script
4. Read the instructions & acknowledgement window
  

SECTION: Running the Script
5. Ensure a time-series file is open, and is at "Top Level" (i.e. select the window) before clicking ok.
  

SECTION: Running the Script
6. Select which Channel(s) you would like to include in the run. There is also the option to include a merged channel (ticked by default).
Images added to the clipboard can also be saved in a folder for later recalling if needed.   

SECTION: Running the Script
7. Choose an Output Directory location.
  

SECTION: Running the Script
8. Move to the desired timepoint (in the image window), and then click OK.
  

SECTION: Running the Script
9. Merged Channel now copied, return when pasted and click OK.
 
Navigate to your program of choice (e.g. Microscoft PowerPoint or Adobe Illustrator/In Design and paste the image from the clipboard. Then click OK. 

SECTION: Running the Script
10. Channel 1 now copied, return when pasted and click OK.

Still in your program of choice, you can paste in the image file without going back to FIJI.

Then click OK.

  

SECTION: Running the Script
11. Repeat for however many channels were selected in the window in Step 6.
  

SECTION: Running the Script
12. Do you have more timepoints?
If you require more timepoints to be selected, leave the Checkbox selected and click OK.
  

SECTION: Running the Script
13. Move to the desired timepoint (using the sliders in the image window), and then click OK.
  

SECTION: Running the Script
14. Repeat Steps 9-11 by pasting the images into your program of choice.
  

SECTION: Running the Script
15. Repeat Steps 8-14 for as many timepoints as you desire.
When finished uncheck the box on the Do you have more timepoints? window.
  

SECTION: Running the Script
16. Batch Completed. Put down that coffee! Your analysis is finished, dialog will appear to inform you of the safe completion of the program. Note the log file also records which frames and the corresponding time value for that frame to help annoting the figure.
  

SECTION: Running the Script
17. Navigate to the output directory location to access your saved files.
Note the log is also saved with the frame number and timepoint information.
  

SECTION: Running the Script
7. Move to the desired timepoint (in the image window), and then click OK.
 
SECTION: Running the Script
8. Merged Channel now copied, return when pasted and click OK.
 
Navigate to your program of choice (e.g. Microscoft PowerPoint or Adobe Illustrator/In Design and paste the image from the clipboard. Then click OK. 

SECTION: Running the Script
9. Channel 1 now copied, return when pasted and click OK.

Still in your program of choice, you can paste in the image file without going back to FIJI.

Then click OK.

  
SECTION: Running the Script
10. Repeat for however many channels were selected in the window in Step 6.
 
SECTION: Running the Script
11. Do you have more timepoints?
If you require more timepoints to be selected, leave the Checkbox selected and click OK.
 
SECTION: Running the Script
12. Move to the desired timepoint (using the sliders in the image window), and then click OK.
  
SECTION: Running the Script
13. Repeat Steps 8-10 by pasting the images into your program of choice.
 
SECTION: Running the Script
14. Repeat Steps 7-13 for as many timepoints as you desire.
When finished uncheck the box on the Do you have more timepoints? window.
  
SECTION: Running the Script
15. Batch Completed. Put down that coffee! Your analysis is finished, dialog will appear to inform you of the safe completion of the program. Note the log file also records which frames and the corresponding time value for that frame to help annoting the figure.