Estimates non-uniform background level by fitting a parametric surface to background samples.

This ImageJ plugin allows removal of a non-uniform background. It finds a least-squares fit of background samples within the image to one of two intensity profiles: 1) a plane, or 2) a 2D cubic polynomial. The estimated background is subtracted from the input image. This plugin can operate on either the current image in a stack or on an entire stack. In the case that it operates on the stack, background fitting operates on a slice-by-slice basis. Additionally, the background estimate image may be created to inspect the quality of the fit.

The plugin will calculate its background image from all ROIs listed in the ROI manager. Therefore, one must first designate regions of interest by using the ROI manager. Ideally, the regions of interest will be dispersed across the entire image. Selecting only a local region of the image may produce a worse fitting background estimate of the image the more distant it gets from this local ROI. This is due to the fit being an extrapolation then of the locally chosen region rather than being a more accurate interpolation between a spatially wider spread variety of regions.

During subtraction of the estimated background from the input image, some negative values could be created. Because these negative values would get clamped to zero (which is undesirable), the plugin computes the minimum of such negative value and offsets ALL corrected values by the absolute value of this minimum. The result is that the minimum value in the corrected stack will be 0.

Another way to remove background from images is the Remove Background command. However, this is based on a rolling ball operation and can not be specified for certain regions of interest. This plugin here is more flexible and might produce more desirable background correction, but it also requires more user input.

Both the non-uniform background removal and the remove background command methods can be used as well for multiplicative background removal rather than their subtractive standard setting. For that purpose the tickboxes only create background must be switched on and the original image later divided through the background image with a result in 32bit.

Download this plugin: Original link broken http://www.cs.unc.edu/~cquammen/imagej/nonuniform_background_removal.html

See this post instead:forum post

— Cory Quammen 2007/08/30 15:45