Dataset Information

Void sorcerer: an open source, open access framework for mouse uroflowmetry.

ABSTRACT: Observational and experimental studies of rodent voiding behaviors have greatly contributed to our understanding of lower urinary tract function including the complex social, environmental, and internal stimuli that affect voiding in health and models of disease. Void spot assays (VSA), cystometry (awake or anesthetized), and uroflowmetry are techniques commonly used in rodent models to assess voiding. Uroflowmetry is non-invasive and can be performed multiple times in the same freely moving animals and can be used to generate synchronized video corresponding to each void to characterize micturition patterns (e.g., droplets versus solid stream). However, approaches to evaluate uroflowmetry in rodent models vary widely across laboratories. Most importantly, an open access software to run these tests is not freely available (although complete systems are commercially available), limiting use of this important assay. We developed the Void Sorcerer, an uroflowmetry system for mice for reliable determination of frequency, voided volume, voiding duration, interval times between micturitions, and flow rate. This report provides a detailed description of how to build this system and includes open access software for developing uroflowmetry capability in their laboratories and improve upon it in a cost-effective manner. Our goals are to improve access, increase reproducibility among laboratories, and facilitate standardizing testing procedures.

SUBMITTER: Wang Z

PROVIDER: S-EPMC6627548 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Void sorcerer: an open source, open access framework for mouse uroflowmetry.

Wang Zunyi Z Guzman Emmanuel Contreras EC Nimunkar Amit A Keil Kimberly P KP Vezina Chad M CM Ricke William A WA Macoska Jill J Bjorling Dale E DE

American journal of clinical and experimental urology 20190615 3

Observational and experimental studies of rodent voiding behaviors have greatly contributed to our understanding of lower urinary tract function including the complex social, environmental, and internal stimuli that affect voiding in health and models of disease. Void spot assays (VSA), cystometry (awake or anesthetized), and uroflowmetry are techniques commonly used in rodent models to assess voiding. Uroflowmetry is non-invasive and can be performed multiple times in the same freely moving ani ...[more]

PMID: 31317056

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Project description:Advances in microscopy technology have led to the creation of high-throughput microscopes that are capable of generating several hundred gigabytes of images in a few days. Analyzing such wealth of data manually is nearly impossible and requires an automated approach. There are at present a number of open-source and commercial software packages that allow the user to apply algorithms of different degrees of sophistication to the images and extract desired metrics. However, the types of metrics that can be extracted are severely limited by the specific image processing algorithms that the application implements, and by the expertise of the user. In most commercial software, code unavailability prevents implementation by the end user of newly developed algorithms better suited for a particular type of imaging assay. While it is possible to implement new algorithms in open-source software, rewiring an image processing application requires a high degree of expertise. To obviate these limitations, we have developed an open-source high-throughput application that allows implementation of different biological assays such as cell tracking or ancestry recording, through the use of small, relatively simple image processing modules connected into sophisticated imaging pipelines. By connecting modules, non-expert users can apply the particular combination of well-established and novel algorithms developed by us and others that are best suited for each individual assay type. In addition, our data exploration and visualization modules make it easy to discover or select specific cell phenotypes from a heterogeneous population.CellAnimation is distributed under the Creative Commons Attribution-NonCommercial 3.0 Unported license (http://creativecommons.org/licenses/by-nc/3.0/). CellAnimationsource code and documentation may be downloaded from www.vanderbilt.edu/viibre/software/documents/CellAnimation.zip. Sample data are available at www.vanderbilt.edu/viibre/software/documents/movies.zip.walter.georgescu@vanderbilt.eduSupplementary data available at Bioinformatics online.

Dataset Information

Void sorcerer: an open source, open access framework for mouse uroflowmetry.

Publications

Void sorcerer: an open source, open access framework for mouse uroflowmetry.

Similar Datasets

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