The formation processes and the evolutionary stages of high-mass stars are poorly understood compared to low-mass stars. Large-scale surveys are needed to provide an unbiased census of high column density sites which can potentially host precursors to high-mass stars. The ATLASGAL survey covers 420 sq. degree of the Galactic plane, between -80{deg}<l<+60{deg} at 870um. Here we identify the population of embedded sources throughout the inner Galaxy. With this catalog we first investigate the general statistical properties of dust condensations in terms of their observed parameters, such as flux density and angular size. Then using mid-IR surveys we aim to investigate their star-formation activity and the Galactic distribution of star-forming and quiescent clumps. Our ultimate goal is to determine the statistical properties of quiescent and star-forming clumps within the Galaxy and to constrain the star-formation processes. We optimized the source extraction method, referred to as MRE-GCL, for the ATLASGAL maps in order to generate a catalog of compact sources. This technique is based on a multi-scale filtering to remove extended emission from clouds to better determine the parameters corresponding to the embedded compact sources. In a second step we extract the sources by fitting 2D Gaussians with the Gaussclumps algorithm.