Automating cell detection and classification in human brain fluorescent microscopy images using dictionary learning and sparse coding

• Published in: Journal of neuroscience methods Vol. 282; no. C; pp. 20 - 33
• Main Authors: Alegro, Maryana, Theofilas, Panagiotis, Nguy, Austin, Castruita, Patricia A., Seeley, William, Heinsen, Helmut, Ushizima, Daniela M., Grinberg, Lea T.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 15.04.2017; Elsevier
• Subjects: Alzheimer Disease - pathology; Brain - cytology; Cell Count - methods; Dictionary learning; Fluorescent Antibody Technique - methods; Humans; Image Processing, Computer-Assisted - methods; Image segmentation; Immunofluorescence; Machine Learning; Microscopy; Microscopy, Fluorescence - methods; Pattern Recognition, Automated - methods; Postmortem human brain; Reproducibility of Results; Sparse models; Image segmentation; Microscopy; Sparse models; Immunofluorescence; Postmortem human brain; Dictionary learning
• ISSN: 0165-0270; 1872-678X
• DOI: 10.1016/j.jneumeth.2017.03.002

•Our method detects and classifies cells in human brain fluorescence microscopy.•Dictionary learning and sparse coding learn to better represent cells in our images.•Segmented cells are automatically classified to speed up the cell counting process.•Our method outperforms several open-access methods in literature.•Efficient cell detection can be used in several fluorescence analysis tasks. Immunofluorescence (IF) plays a major role in quantifying protein expression in situ and understanding cell function. It is widely applied in assessing disease mechanisms and in drug discovery research. Automation of IF analysis can transform studies using experimental cell models. However, IF analysis of postmortem human tissue relies mostly on manual interaction, often subjected to low-throughput and prone to error, leading to low inter and intra-observer reproducibility. Human postmortem brain samples challenges neuroscientists because of the high level of autofluorescence caused by accumulation of lipofuscin pigment during aging, hindering systematic analyses. We propose a method for automating cell counting and classification in IF microscopy of human postmortem brains. Our algorithm speeds up the quantification task while improving reproducibility. Dictionary learning and sparse coding allow for constructing improved cell representations using IF images. These models are input for detection and segmentation methods. Classification occurs by means of color distances between cells and a learned set. Our method successfully detected and classified cells in 49 human brain images. We evaluated our results regarding true positive, false positive, false negative, precision, recall, false positive rate and F1 score metrics. We also measured user-experience and time saved compared to manual countings. We compared our results to four open-access IF-based cell-counting tools available in the literature. Our method showed improved accuracy for all data samples. The proposed method satisfactorily detects and classifies cells from human postmortem brain IF images, with potential to be generalized for applications in other counting tasks.