example of measuring intensity through time

Author: Michael Cammer mcammer@gmail.com
History: First version 20170411 for measuring intensity through time of low magnification (20X N.A. 0.65) Ca++ imaging with Fluo4 by widefield



It's just a macro. Plugins > Macros > Install...
Or open as a text file and install or run from the menu at the top of the window. (If you're uing real IJ.)


Macro expects two windows open.
1. A single channel stack with XY images through time. This window must be the active window. (Other images may be open too.)
2. ROI Manager window populated with ROIs to be intensity measured through time.
To get ROIs quickly, we recommend making a maximum pixel projection through time.
Then using threshold and magic wand tool to add cells that are not touching and manually tracing to add cells that are touching.

Output is columns of tab delimitted numbers that may be saved as text file or copy and pasted into favorite spreadsheet program.

In this version, bg subtraction would be of a constant. Because ROIs may touch, difficult to automate for a local bg subtraction, but could be implemented including bg calculated at each timepoint.

If firing not coordinated, ImageJ does have the ability to find the peak timepoint intensity and align all the plots to this peak.

See Also:

Macro for measuring the brightest n% of pixels in a given area to measure Ca++ in moving objects against a black bg.


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