title: Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis.
abstract: With the realization that bacteria display phenotypic variability among cells and exhibit complex subcellular organization critical for cellular function and behavior, microscopy has re-emerged as a primary tool in bacterial research during the last decade. However, the bottleneck in today's single-cell studies is quantitative image analysis of cells and fluorescent signals. Here, we address current limitations through the development of Oufti, a stand-alone, open-source software package for automated measurements of microbial cells and fluorescence signals from microscopy images. Oufti provides computational solutions for tracking touching cells in confluent samples, handles various cell morphologies, offers algorithms for quantitative analysis of both diffraction and non-diffraction-limited fluorescence signals and is scalable for high-throughput analysis of massive datasets, all with subpixel precision. All functionalities are integrated in a single package. The graphical user interface, which includes interactive modules for segmentation, image analysis and post-processing analysis, makes the software broadly accessible to users irrespective of their computational skills.
authors.affiliation: Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA.|Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520, USA.
authors.forename: Ahmad
authors.initials: A
authors.lastname: Paintdakhi
authors.affiliation: Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA.|Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520, USA.|Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA.
authors.forename: Bradley
authors.initials: B
authors.lastname: Parry
authors.affiliation: Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA.|Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520, USA.|Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA.
authors.forename: Manuel
authors.initials: M
authors.lastname: Campos
authors.affiliation: Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA.|Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520, USA.|Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA.
authors.forename: Irnov
authors.initials: I
authors.lastname: Irnov
authors.affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Elf
authors.affiliation: Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA.|Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520, USA.|Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA.
authors.forename: Ivan
authors.initials: I
authors.lastname: Surovtsev
authors.affiliation: Microbial Sciences Institute, Yale University, West Haven, CT, 06516, USA.|Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520, USA.|Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA.|Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, 06510, USA.
authors.forename: Christine
authors.initials: C
authors.lastname: Jacobs-Wagner
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000166:cytology* / Q000648:ultrastructure; D019295:Computational Biology; D000068598:Data Accuracy; D057166:High-Throughput Screening Assays; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008856:Microscopy, Fluorescence; D012984:Software