Is there a function to label connected regions? Or should I use FloodFill to fill each connected region with a label?
FloodFill function sets to a value a connected region with the same pixel value as the seed pixel. FloodFill_Range and FloodFill_Grad treat as a region a set of pixels in the interval or a set of pixels with restricted gradient. I think it is not just what ask.
If connected regions are connected sets of neighboring non-zero pixels you can use ippiLabelMarkers_8u_C1IR function that assigns the same unique value from [1,254] to all pixels of different connected components. This function is included to IPP 5.2 Beta.