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WormSizer specifications

Information


Unique identifier OMICS_23469
Name WormSizer
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++, Java
License BSD 2-clause “Simplified” License
Computer skills Medium
Version 1.2.5
Stability Stable
Requirements
ImageJ/Fiji
Maintained Yes

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Publication for WormSizer

WormSizer in publications

 (7)
PMCID: 5543044
PMID: 28775277
DOI: 10.1038/s41598-017-07455-7

[…] were performed on synchronized adult animals four days after bleaching. measurements were made of 12 animals grown on agar, 13 grown on ngg, and 10 in liquid culture using the imagej plug-in wormsizer. box plots in supplementary figure  show quartile edges (25% and 75%) of the distribution and medians (black bars), made in r {boxplot(shape~condition, data = worm_sizes, horizontal = true, […]

PMCID: 5540977
PMID: 28769037
DOI: 10.1038/s41598-017-07222-8

[…] were taken at l4 larval stage and day 1, 3, 4 of adulthood using zeiss axiozoom.v16 with the set magnification. next, surface area of individual worms was determined by means of imagej software and wormsizer plugin. the recognition of each individual worm by software was reevaluated by eye., 5 to 8 living worms were put into the center of 100 µm deep planchette hats that is filled with yeast […]

PMCID: 5655125
PMID: 29063832
DOI: 10.7554/eLife.30057.038

[…] scientific, waltham, ma). levels of trehalose were normalized to protein. normalizing trehalose content by worm number instead of protein concentration provided qualitatively similar results., the wormsizer plugin for fiji was used to measure the length of worms (). length after 48 hr of development was measured in several genotypes and in the presence of a range of 2-dg […]

PMCID: 5081166
PMID: 27783623
DOI: 10.1371/journal.pgen.1006396

[…] in batch and the results were manually curated to ensure only quality embryo images were used., size of l1 larvae and worms cultured for 48 or 96 hr (starting from l1 arrest) was measured using the wormsizer software []. worms were washed with s-basal and plated on unseeded 10 cm ngm plates. these were imaged with a zeiss discovery.v20 stereomicroscope and magnification was adjusted based […]

PMCID: 4873252
PMID: 27195667
DOI: 10.1371/journal.pone.0151955

[…] automatic methods for measuring curved lengths are susceptible to flaws. in fact, a process called ‘skeletonization’ [, ] is embedded in fiji, and it has already been employed in the application wormsizer [], designed for assessing size and shape of nematodes. although it has worked well with fairly regular tube shapes like worms [], and appears to be suitable for simple-shaped unicellular […]


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WormSizer institution(s)
PhD Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA; Department of Biology, Duke University, Durham, NC, USA; Duke Center for Systems Biology, Duke University, Durham, NC, USA
WormSizer funding source(s)
Supported by The National Science Foundation (IOS-1120206) and by National Institutes of Health Training Grant T32 GM071340.

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