The present invention is an improvement to a computer system for processing, storing and searching DICOM medical imaging objects and non-DICOM files. The improvement is the addition of a directory manager, a user interface and a search manager that allows users to define a hierarchy of directories that link to both DICOM and non-DICOM files. Contents of files are indexed, including metadata so they are searchable. The system automatically creates directories representing DICOM series and studies by analyzing metadata in DICOM image files DICOM devices can send DICOM data directly to directories in the file system using the DICOM protocol.