Context.A possible pathway for understanding the events and the mechanisms involved in galaxy formation and evolution is an in-depth investigation of the galactic and inter-galactic fossil sub-structures with long dynamical timescales: stars in the field and in stellar clusters.Aims.This paper continues the Fornax Deep Survey (FDS) series. Following previous studies dedicated to extended Fornax cluster members, we present the catalogs of compact stellar systems in the Fornax cluster, as well as extended background sources and point-like sources.Methods.We derivedugriphotometry of ∼1.7 million sources over the ∼21 square degree area of FDS centered on the bright central galaxy NGC 1399. For a wider area, of ∼27 square degrees extending in the direction of NGC 1316, we providedgriphotometry for ∼3.1 million sources. To improve the morphological characterization of sources, we generated multi-band image stacks by coadding the best-seeinggri-band single exposures with a cut at full width at half maximum (FWHM) ≤ 0.″9. We used the multi-band stacks as master detection frames, with a FWHM improved by ∼15% and a FWHM variability from field to field reduced by a factor of ∼2.5 compared to the pass-band with the best FWHM, namely ther-band. The identification of compact sources, in particular, globular clusters (GC), was obtained from a combination of photometric (e.g., colors, magnitudes) and morphometric (e.g., concentration index, elongation, effective radius) selection criteria, also taking as reference the properties of sources with well-defined classifications from spectroscopic or high-resolution imaging data.Results.Using the FDS catalogs, we present a preliminary analysis of GC distributions in the Fornax area. The study confirms and extends further previous results that were limited to a smaller survey area. We observed the inter-galactic population of GCs, a population of mainly blue GCs centered on NGC 1399, extending over ∼0.9 Mpc, with an ellipticityϵ ∼ 0.65 and a small tilt in the direction of NGC 1336. Several sub-structures extend over ∼0.5 Mpc along various directions. Two of these structures do not cross any bright galaxy; one of them appears to be connected to NGC 1404, a bright galaxy close to the cluster core and particularly poor in GCs. Using thegricatalogs, we analyze the GC distribution over the extended FDS area and do not find any obvious GC sub-structure bridging the two brightest cluster galaxies, namely, NGC 1316 and NGC 1399. Although NGC 1316 is more than twice as bright of NGC 1399 in optical bands, usinggridata, we estimate a GC population that is richer by a factor of ∼3−4 around NGC 1399, as compared to NGC 1316, out to galactocentric distances of ∼40′ or ∼230 kpc.
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