title: Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library.
abstract: The determination and regulation of cell morphology are critical components of cell-cycle control, fitness, and development in both single-cell and multicellular organisms. Understanding how environmental factors, chemical perturbations, and genetic differences affect cell morphology requires precise, unbiased, and validated measurements of cell-shape features.
  
  
  
  Here we introduce two software packages, Morphometrics and BlurLab, that together enable automated, computationally efficient, unbiased identification of cells and morphological features. We applied these tools to bacterial cells because the small size of these cells and the subtlety of certain morphological changes have thus far obscured correlations between bacterial morphology and genotype. We used an online resource of images of the Keio knockout library of nonessential genes in the Gram-negative bacterium Escherichia coli to demonstrate that cell width, width variability, and length significantly correlate with each other and with drug treatments, nutrient changes, and environmental conditions. Further, we combined morphological classification of genetic variants with genetic meta-analysis to reveal novel connections among gene function, fitness, and cell morphology, thus suggesting potential functions for unknown genes and differences in modes of action of antibiotics.
  
  
  
  Morphometrics and BlurLab set the stage for future quantitative studies of bacterial cell shape and intracellular localization. The previously unappreciated connections between morphological parameters measured with these software packages and the cellular environment point toward novel mechanistic connections among physiological perturbations, cell fitness, and growth.
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.|Department of Physics, University of Oregon, Eugene, OR, 97403, USA.
authors.forename: Tristan
authors.initials: T
authors.lastname: Ursell
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
authors.forename: Timothy K
authors.initials: TK
authors.lastname: Lee
authors.affiliation: National Institute of Genetics, Shizuoka, Japan.|Current address: Department of Life Science, Rikkyo University, Tokyo, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Shiomi
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
authors.forename: Handuo
authors.initials: H
authors.lastname: Shi
authors.affiliation: Biophysics Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.|Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
authors.forename: Carolina
authors.initials: C
authors.lastname: Tropini
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.|Current address: Synthetic Genomics Inc., La Jolla, CA, 92037, USA.
authors.forename: Russell D
authors.initials: RD
authors.lastname: Monds
authors.affiliation: Biophysics Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Colavin
authors.affiliation: Department of Physics, Stanford University, Stanford, CA, 94305, USA.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Billings
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
authors.forename: Ilina
authors.initials: I
authors.lastname: Bhaya-Grossman
authors.affiliation: Department of Computer Science, Stanford University, Stanford, CA, 94305, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Broxton
authors.affiliation: Janssen Research and Development, Menlo Park, CA, 94025, USA.
authors.forename: Bevan Emma
authors.initials: BE
authors.lastname: Huang
authors.affiliation: National Institute of Genetics, Shizuoka, Japan.
authors.forename: Hironori
authors.initials: H
authors.lastname: Niki
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA. kchuang@stanford.edu.|Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA. kchuang@stanford.edu.
authors.forename: Kerwyn Casey
authors.initials: KC
authors.lastname: Huang
mesh_terms: D003198:Computer Simulation; D004926:Escherichia coli / Q000166:cytology* / Q000235:genetics*; D017353:Gene Deletion; D055786:Gene Knockout Techniques; D015723:Gene Library; D016680:Genome, Bacterial; D021621:Imaging, Three-Dimensional; D008856:Microscopy, Fluorescence; D015203:Reproducibility of Results
keywords: Cell biology; Cell morphology; Cell shape; Chemical genomics; Computer vision; Imaging; Microbiology; Microscopy; Principal component analysis; Segmentation