Dataset Information

WormGender - Open-Source Software for Automatic Caenorhabditis elegans Sex Ratio Measurement.

ABSTRACT: Fast and quantitative analysis of animal phenotypes is one of the major challenges of current biology. Here we report the WormGender open-source software, which is designed for accurate quantification of sex ratio in Caenorhabditis elegans. The software functions include, i) automatic recognition and counting of adult hermaphrodites and males, ii) a manual inspection feature that enables manual correction of errors, and iii) flexibility to use new training images to optimize the software for different imaging conditions. We evaluated the performance of our software by comparing manual and automated assessment of sex ratio. Our data showed that the WormGender software provided overall accurate sex ratio measurements. We further demonstrated the usage of WormGender by quantifying the high incidence of male (him) phenotype in 27 mutant strains. Mutants of nine genes (brc-1, C30G12.6, cep-1, coh-3, him-3, him-5, him-8, skr-1, unc-86) showed significant him phenotype. The WormGender is written in Java and can be installed and run on both Windows and Mac platforms. The source code is freely available together with a user manual and sample data at http://www.QuantWorm.org/. The source code and sample data are also available at http://dx.doi.org/10.6084/m9.figshare.1541248.

SUBMITTER: Labocha MK

PROVIDER: S-EPMC4589236 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

WormGender - Open-Source Software for Automatic Caenorhabditis elegans Sex Ratio Measurement.

Labocha Marta K MK Jung Sang-Kyu SK Aleman-Meza Boanerges B Liu Zheng Z Zhong Weiwei W

PloS one 20150930 9

Fast and quantitative analysis of animal phenotypes is one of the major challenges of current biology. Here we report the WormGender open-source software, which is designed for accurate quantification of sex ratio in Caenorhabditis elegans. The software functions include, i) automatic recognition and counting of adult hermaphrodites and males, ii) a manual inspection feature that enables manual correction of errors, and iii) flexibility to use new training images to optimize the software for dif ...[more]

PMID: 26421844

Similar Datasets

Project description:Roots are central to the function of natural and agricultural ecosystems by driving plant acquisition of soil resources and influencing the carbon cycle. Root characteristics like length, diameter and volume are critical to measure to understand plant and soil functions. RhizoVision Explorer is an open-source software designed to enable researchers interested in roots by providing an easy-to-use interface, fast image processing and reliable measurements. The default broken roots mode is intended for roots sampled from pots and soil cores, washed and typically scanned on a flatbed scanner, and provides measurements like length, diameter and volume. The optional whole root mode for complete root systems or root crowns provides additional measurements such as angles, root depth and convex hull. Both modes support providing measurements grouped by defined diameter ranges, the inclusion of multiple regions of interest and batch analysis. RhizoVision Explorer was successfully validated against ground truth data using a new copper wire image set. In comparison, the current reference software, the commercial WinRhizo™, drastically underestimated volume when wires of different diameters were in the same image. Additionally, measurements were compared with WinRhizo™ and IJ_Rhizo using a simulated root image set, showing general agreement in software measurements, except for root volume. Finally, scanned root image sets acquired in different labs for the crop, herbaceous and tree species were used to compare results from RhizoVision Explorer with WinRhizo™. The two software showed general agreement, except that WinRhizo™ substantially underestimated root volume relative to RhizoVision Explorer. In the current context of rapidly growing interest in root science, RhizoVision Explorer intends to become a reference software, improve the overall accuracy and replicability of root trait measurements and provide a foundation for collaborative improvement and reliable access to all.

Project description:BackgroundInertial measurements (IMUs) facilitate the measurement of human motion outside the motion laboratory. A commonly used open-source software for musculoskeletal simulation and analysis of human motion, OpenSim, includes a tool to enable kinematics analysis of IMU data. However, it only enables offline analysis, i.e., analysis after the data has been collected. Extending OpenSim's functionality to allow real-time kinematics analysis would allow real-time feedback for the subject during the measurement session and has uses in e.g., rehabilitation, robotics, and ergonomics.MethodsWe developed an open-source software library for real-time inverse kinematics (IK) analysis of IMU data using OpenSim. The software library reads data from IMUs and uses multithreading for concurrent calculation of IK. Its operation delays and throughputs were measured with a varying number of IMUs and parallel computing IK threads using two different musculoskeletal models, one a lower-body and torso model and the other a full-body model. We published the code under an open-source license on GitHub.ResultsA standard desktop computer calculated full-body inverse kinematics from treadmill walking at 1.5 m/s with data from 12 IMUs in real-time with a mean delay below 55 ms and reached a throughput of more than 90 samples per second. A laptop computer had similar delays and reached a throughput above 60 samples per second with treadmill walking. Minimal walking kinematics, motion of lower extremities and torso, were calculated from treadmill walking data in real-time with a throughput of 130 samples per second on the laptop and 180 samples per second on the desktop computer, with approximately half the delay of full-body kinematics.ConclusionsThe software library enabled real-time inverse kinematical analysis with different numbers of IMUs and customizable musculoskeletal models. The performance results show that subject-specific full-body motion analysis is feasible in real-time, while a laptop computer and IMUs allowed the use of the method outside the motion laboratory.

Dataset Information

WormGender - Open-Source Software for Automatic Caenorhabditis elegans Sex Ratio Measurement.

Publications

WormGender - Open-Source Software for Automatic Caenorhabditis elegans Sex Ratio Measurement.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets