title: Automating cell detection and classification in human brain fluorescent microscopy images using dictionary learning and sparse coding.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Memory and Aging Center, University of California San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA. Electronic address: maryana.alegro@ucsf.edu.
authors.forename: Maryana
authors.initials: M
authors.lastname: Alegro
authors.affiliation: Memory and Aging Center, University of California San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA. Electronic address: panos.theofilas@ucsf.edu.
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Theofilas
authors.affiliation: Memory and Aging Center, University of California San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA. Electronic address: austin.nguy@ucsf.edu.
authors.forename: Austin
authors.initials: A
authors.lastname: Nguy
authors.affiliation: Memory and Aging Center, University of California San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA. Electronic address: alejandra.castcap@gmail.com.
authors.forename: Patricia A
authors.initials: PA
authors.lastname: Castruita
authors.affiliation: Memory and Aging Center, University of California San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA. Electronic address: bill.seeley@ucsf.edu.
authors.forename: William
authors.initials: W
authors.lastname: Seeley
authors.affiliation: Medical School of the University of São Paulo, Av. Reboucas 381, São Paulo, SP 05401-000, Brazil. Electronic address: heinsen@mail.uni-wuerzburg.de.
authors.forename: Helmut
authors.initials: H
authors.lastname: Heinsen
authors.affiliation: Computational Research Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA; Berkeley Institute for Data Science, University of California Berkeley, Berkeley, CA 94720, USA. Electronic address: dushizima@lbl.gov.
authors.forename: Daniela M
authors.initials: DM
authors.lastname: Ushizima
authors.affiliation: Memory and Aging Center, University of California San Francisco, 675 Nelson Rising Lane, San Francisco, CA 94158, USA. Electronic address: lea.grinberg@ucsf.edu.
authors.forename: Lea T
authors.initials: LT
authors.lastname: Grinberg
mesh_terms: D000544:Alzheimer Disease / Q000473:pathology; D001921:Brain / Q000166:cytology*; D002452:Cell Count / Q000379:methods; D005455:Fluorescent Antibody Technique / Q000379:methods; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D000069550:Machine Learning; D008856:Microscopy, Fluorescence / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results
keywords: Dictionary learning; Image segmentation; Immunofluorescence; Microscopy; Postmortem human brain; Sparse models