ImageJ Macros

Repository of ImageJ scripts used in image processing by the Yang Lab at the University of Michigan

Current scripts

• Make_FRET_Ratio_video.ijm: Creates AVI videos of the FRET Ratio signal for single or multiple microscope positions. FRET and CFP channels needed.

Temperature

• Open_resize_straighten_images.ijm: Create new tiff files from raw data that only contain a single tube.
• FRET_ratio_video.ijm: Create a video of the FRET ratio signal for a single or multiple microscope positions. FRET and CFP channels needed.
• flip_save_avi.ijm: Flip and save a video as an AVI file. Used after FRET_ratio_video.ijm to flip the video so that the temperature is increasing from left to right.
• combine_fret_videos.ijm: Combine all videos belonging to the same row of a temperature experiment. Save the result as a tiff.
• make_montage.ijm: Create a montage of the vertical average of a tube over time (kymograph).
• combine_tube_montages.ijm: Combine all montages belonging to the same row of a temperature experiment. Save the result as a tiff.

Installation

The scripts can be run using two methods:

1. Open the script as a file in ImageJ's editor and click 'Run'
2. Copy the contents of script into ImageJ's script folder (found in ImageJ's installation directory). This method incorporates the scripts into ImageJ's Plugins/Scripts menu.