We proposed an image retrieval algorithm that deals with multi-instance query with heterogeneous features. For the pre-processing, we utilized the gray-level morphological operations by reconstruction to effectively identify the foreground objects in images. This method can be processed by the pipeline architecture which is suitable for dealing with volume images. The retrieval process is carried out in intra and inter feature domains: (1) the intra retrieval utilizes the profession of multi-instance query with one feature and; (2) the inter retrieval coordinates the individual intra retrieval results to boost salient common features among query samples. To represent feature saliency, the averaged normalized correlation coefficient is computed in the intra domain and is normalized in the inter domain. The most distinguished point of this algorithm is that it coordinates heterogeneous features for multi-instance retrieval. Up to five different image types could be integrated for retrieval. Simulations demonstrate satisfactory subjective and objective retrieval performances.