Zirmi

Zirmi is a software tool to analyze macrophage behavior in zebrafish reporter-based assays. It provides an image analysis pipeline that enables real-time quantitative measurements of cellular kinetics and reactive oxygen species (ROS) content in macrophages. This tool addresses the current limitations of commercially available software solutions in detecting and quantifying macrophage responses to oxidative stress.

Key features of Zirmi include:

1. Real-time analysis of macrophage migration and behavior in response to tissue injury and biochemical cues, such as ROS.

2. Quantitative measurements of cellular kinetics, allowing for a better understanding of macrophage movement and activity.

3. Detection and quantification of ROS content within macrophages, providing insights into their response to oxidative stress.

4. Compatibility with zebrafish reporter-based assays, which are increasingly used in the study of macrophage behavior.

Topic

Workflows;Imaging;Transcription factors and regulatory sites

Detail

  • Operation: Quantification

  • Software interface: Command-line user interface

  • Language: MATLAB

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: The Diversify Higher Education Faculty in Illinois Fellowship and the UIC Department of Surgery.

  • Input: -

  • Output: -

  • Contact: Andre D. Paredes apared3@uic.edu

  • Collection: -

  • Maturity: -

Publications

  • An automated quantitative image analysis pipeline of in vivo oxidative stress and macrophage kinetics.
  • Paredes AD, et al. An automated quantitative image analysis pipeline of in vivo oxidative stress and macrophage kinetics. An automated quantitative image analysis pipeline of in vivo oxidative stress and macrophage kinetics. 2018; 5:e101. doi: 10.14440/jbm.2018.259
  • https://doi.org/10.14440/JBM.2018.259
  • PMID: 31453251
  • PMC: PMC6706154

Download and documentation

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