Oufti protocols

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Oufti specifications

Information


Unique identifier OMICS_26045
Name Oufti
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Mac OS, Windows
Programming languages MATLAB
Computer skills Medium
Stability Stable
Registration required Yes
Maintained Yes

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Maintainer


  • person_outline Christine Jacobs-Wagner <>

Additional information


http://oufti.org/tutorial.htm

Publication for Oufti

Oufti in pipelines

 (3)
2017
PMCID: 5320674
PMID: 28222723
DOI: 10.1186/s12915-017-0348-8

[…] and superior cell-division classification using objectj [, ]. another software package, microbetracker, enabled segmentation of cells within a dense population []; microbetracker and its successor oufti [] were recently used to investigate the relationships among growth rate, elongation, and division in e. coli [] and caulobacter crescentus [, ]. for rod-shaped bacteria, most quantitative […]

2016
PMCID: 5096676
PMID: 27814364
DOI: 10.1371/journal.pcbi.1005177

[…] operations, thresholding, and the watershed transform—from computer vision. typically, a combination of these tools are tailored to each individual experiment [, –]. for example, cellprofiler and oufti are tools to perform cell segmentation and tracking (primarily using thresholding, watershed transform, and voronoi algorithms). supervised machine learning methods have also seen significant […]

2016
PMCID: 5096676
PMID: 27814364
DOI: 10.1371/journal.pcbi.1005177

[…] use highly-tuned combinations of these standard techniques to solve the image segmentation problem for specific experiments, there is a barrier to sharing work and ideas in this space. cellprofiler, oufti, and ilastik represent notable exceptions, and have empowered a number of experiments, including in labs which were otherwise new to computational image analysis [, , ]. however, the overall […]


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Oufti in publications

 (8)
PMCID: 5829741
PMID: 29294118
DOI: 10.1093/nar/gkx1290

[…] on the pad and once cells were absorbed onto the m9-agarose the pad was placed on the microscope slide and imaged., bacterial cells in phase-contrast images were segmented using matlab and oufti package (). foci were detected using a crocker and grier routine (adapted for matlab by blair and dufresne, http://site.physics.georgetown.edu/matlab/) embedded in a custom automated […]

PMCID: 5636887
PMID: 29021534
DOI: 10.1038/s41467-017-00903-y

[…] time-lapse videos were recorded by taking images every min after inoculation unless specified otherwise. file conversions were done using fiji and analysis of the resulting images was done using oufti., a mathematical model of the network of competence regulation (fig. ) was developed as a system of odes. the model incorporates the protein interactions involved in sensing csp via […]

PMCID: 5607218
PMID: 28886022
DOI: 10.1371/journal.pgen.1006999

[…] for yfp and et-ecfp for cfp, et-dsred for mcherry and et-ecfp for hada. images were processed in adobe photoshop. automated cell length analysis was performed and demographs were generated using oufti or microbej [,]., cells from eg864, eg1133, and eg1863 were grown in pye and prepared for whole cell tem exactly as described []., the length of each constriction (cell-cell connection) […]

PMCID: 5578688
PMID: 28827812
DOI: 10.1371/journal.pgen.1006978

[…] v2 digital cmos camera (hamamatsu photonics, hamamatsu city, japan). all images were acquired using metamorph software (molecular devices, sunnyvale, ca, usa), and analyzed with metamorph, oufti [] and matlab software (mathworks)., genomic dna (gdna) was extracted using chargeswitch kit (thermo fisher scientific) from overnight cultures of the δhfq strain (cjw5477) grown in pye at 30°c […]

PMCID: 5379763
PMID: 28376782
DOI: 10.1186/s12918-017-0399-z

[…] and computer vision []. for bacterial image processing, well known open source software packages for analyzing cell movies are the tlm-tracker [], celltracer [], microbetracker [] and its successor oufti [], and schnitzcells []. the tlm-tracker [] uses multiple alternative algorithms for cell segmentation, such as threshold-based, watershed transform and level-set methods. to construct […]


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Oufti institution(s)
Microbial Sciences Institute, Yale University, West Haven, CT, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA; Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
Oufti funding source(s)
Supported by the National Institutes of Health (R01 GM065835).

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