In Fiji you could do the following:
- Invert the image with
Edit > Invert
. - Select the point selection tool from the Fiji toolbar.
- Click in the region you want to extract the connected white pixels from, to place a point selection there.
- Run
Plugins > Process > Find Connected Regions
. - Select
Start from point selection?
and changeStop after this number of regions are found
to1
. - Click
OK
.
There's some documentation for that plugin (which I wrote a long time ago). It uses a very naive algorithm for finding connected regions, but it's good enough for many purposes.