I am trying to get the plot profile of my bands in ImageJ (FIJI). My method of quantification involves the following steps: I use the rectangle tool in Imagej but because the gel transferred somewhat at an angle I have to use the Selection Rotator plugin to adjust my rectangle (and make sure I capture all the lanes as accurately as possible). However, when I hit "K" to get the Plot profile, I get the message "Line or Rectangular selection required," does anyone know how to move past this message to obtain the plot profile with the peak intensities? I have consulted with ImageJ documents that do not specify how to move past this issue.
Using solely the rectangle tool without rotating it to correctly get my lanes included as tightly as possible would make my plots less accurate, so I would like to figure out how I can get past this error message and get a plot that is truly representative of my data. Any help would be greatly appreciated.
Plotting intensity of a rectangular ROI requires a rectangular array for the code to work. If you rotate an ROI box, the structure of the array is no longer valid. Try using the rotate transform on the image instead. This way you can create the rectangular array for the plot. The other possibility is to write your own macro to plot a line and then move the line pixel by pixel until you have covered the desired area. Then you can assemble the data into an area plot that is skewed at any angle.
Hi,
Selection rotator plugin might not compatible with profile plotting.
Though you can use line selection widening the line to the size you need up to a certain limit around 100 pixels.
Just double click line selection icon then you can set the selection width.
Then you will get the profile averaged over the selected width.
This way you can easily select line in any angle and plot its profile.
Hope this helps.
Best,
Zoltan
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