Ultrastructure of nucleolar DNA is most important to elucidate transcription site of rRNA. Many judgments were made in this respect but all of them were based on direct experimental observations. A new technology for the quantitative analysis of the location of nucleolar DNA in situ from EM data of the ultrastructure of the nucleolus in allium sativum cells and from the modified NAMA-Ur DNA specific staining method was developed. For this purpose, a new methodology of multi-scale morphological gradient operator and automatic analysis software named “HEREN.CELL” were created and adopted. By using this method, superfine contour of the nucleolar ultrastruture was obtained and showed the location and location of nucleolar DNA in situ. From the results, a “petaline envelope” model was proposed, which indicated that nucleolar DNA fibrils radiate from center to periphery of the nucleolus. The study will contribute to the development of the EM image processing technology and the study of nucleolar ultrastructure of the nucleolus.