Hi Michael,
Top-hat transform may work well. It is morphological filtering
operator, unlike linear filtering operator. MATLAB documentation shows
an example: http://www.mathworks.com/access/helpdesk/help/toolbox/images/imtophat.html

It works like this.
- morphological opening removes structures smaller than given mask
(structuring element) from the image. If you pick up a circular mask
slightly larger than cell, the opening operation will remove cells and
retain background.
- Subtracting the background should then leave cells on 'flat
background'. MATLAB example above removes background from a rice
image.
If background is smoother than cells of interest, above method works
almost always.
ImageJ has morphological opening function under Binary menu (I think).

best
Shalin
On Sun, Mar 21, 2010 at 8:13 AM, MODEL, MICHAEL <[log in to unmask]> wrote:
> Hello,
>
>  Does anyone know of a background subtraction method that would act like this:
>
> 1) find the entire area occupied by a cell (automatically or manually)
> 2) reconstruct the background under a cell by interpolation from the outer boundary into the area occupied by a cell.
> 3) subtract the restored background from the original
>
> Other and simpler background removal methods of which I know are based on filters and aren't precise enough. Thanks!
>
> Mike