The tool finds the background intensity value and subtract it from the current image. It searches for the maximum intensity value around pixels that are below or equal to the minimum intensity in the image plus an offset.

Getting started

To install the tool save the file find_and_subtract_background.ijm into the folder macros/toolsets of your FIJI installation.

Select the "find_and_subtract_background" tool from the >> button of the ImageJ launcher.

A left-click on the button runs the tool on the current image. A right-click opens the options-dialog.

Method

The tool looks for the maximum intensity in a neighbourhood of the given radius around pixel with an intensity value below or equal to the minimum intensity in the image plus an offset. The procedure can be repeated multiple times. When a given ratio of intensities is zero the operation is skipped.

Options

• radius - the radius around the pixels below the minimum+offset in which the maximum is searched
• offset - the maximum is searched around pixels with an intensity<=min+offset
• iterations - the number of times the operation is repeated
• skip limit - the ratio of pixels with a zero intensity above which the operation is skipped