This project propose hyper reflective foci (HFs) is related to retinal disease progression, and the quantity has proven to be a prognostic factor of visual and anatomical outcome in various retinal diseases. However, lack of efficient quantitative tools for evaluating the HFs has deprived ophthalmologist of assessing the volume of HFs. For this reason, we propose an automated quantification algorithm to segment and quantify HFs in spectral domain optical coherence tomography (SD-OCT). The proposed algorithm consists of two parallel processes namely: region of interest (ROI) generation and HFs estimation. To generate the ROI, we use morphological reconstruction (MR) to obtain the reconstructed image and histogram constructed for data distributions and clustering. In parallel, we estimate the HFs by extracting the external regions from the connected regions obtained from a component tree. Finally, both the ROI and the HFs estimation process are merged to obtain the segmented HFs. The proposed algorithm was tested on 40 3D SD-OCT volumes from 40 patients diagnosed with non-proliferative diabetic retinopathy (NPDR), proliferative diabetic retinopathy (PDR) and diabetic macular edema (DME). The average dice similarity coefficient (DSC) and correlation coefficient (r) are 69.70%, 0.99 for NPDR, 70.31%, 0.99 for PDR, and 71.30%, 0.99 for DME respectively. The proposed algorithm can provide ophthalmologist with good HFs quantitative information, such as volume, size and location of the HFs. This project is implemented with MATLAB software.