WhiskerTrackering is a set of Fiji plugins and macros for tracking a single whisker.
- Make sure that your Fiji version is up to date (Help > update ImageJ). These macros also require some plugins which may not be included in old Fiji versions.
- ffmpeg is requried to import movies. Install it if you have not done so.
- Install Whisker_Trackering using ImageJ updater. Open Fiji, "Help" > "Update" > "Manage update sites" > select "WhsiketTracking" > "Close" > "Apply changes" in "ImageJ Updater".
- Restart Fiji.
- I recommend you assign short cut keys to plugins in WhiskerTrackering ("Plugins" > "Shortcuts" > "Add Shortcut").
- The program expects grayscale, white-background (high pixel value) movies. Good image quality is crucial for correct tracking. I use the Optronis 600x2 camera, Navitar 50mm lens
(f/1.4), and an 2x expansion lens (EX2C, Edmund Optics). The whisker is illuminated
using an infrared LED (M850L2-C1, Thorlabs).
- Run A_Make_Background. Select a movie, and epoch where whisker is moving. This macro generates a background image used in the following plugins.
- Use B_Track_Whisker. Choose all the movies to process. You are prompted to set the base coordinate for whisker base, radius, and angles. This plugin generates a profile image for each movie. In this image, each column corresponds to a profile on the arc of a frame. The darkest points in each column are connected.
- Open a profile image, and run C_Profile_To_Trace to convert the image data to text file containing an angle array. Remove any incorrectly tracked points by a. making an roi, and b. backspace or edit > clear (create a shortcut!).
- If the tracking is not good, you can manually correct the result using D_Inspect_On_Movie. Check whisker position in each frame. Correct whisker position with a left click. Right click the image when you are done.
- The resulting text file can be directly copied and pasted in Matlab.
- If this software is useful to you, I would appreciate it if you acknowledged it with my paper in prep..
