An optical inspection tool can automatically perform analysis/operations after the tool has generated data identifying defects (e.g. a defect list) from an inspection run of an object such as a semiconductor wafer. The tool can decouple post-inspection tasks from performing inspection runs so that one or more post-inspection tasks are performed on defect data from a previous inspection run while another inspection run is in progress. This can significantly improve the throughput of the tool when multiple inspections are performed, since the inspection run time effectively is shortened to include only the time the tool is actually used to acquire defect data. One or more post-inspection tasks can be performed, including, but not limited to, merging inspection runs, removing duplicate defects, removing straight-line false alarms, and characterizing defects.