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This site contains the project documentation for the 'Polony Counter Project'

Introduction to Polony Counter

Welcome to the documentation for the Polony Counter project! This tool is designed to revolutionize the way viruses are quantified in marine water samples, offering a sophisticated yet user-friendly solution for researchers and scientists in the field of marine biology and virology.

What is Polony?

Polony is a solid-phase single-molecule PCR-based method originally developed by Mitra and Church in 1999. In 2018 by Baran et.al. at Lindell lab, Technion it was adapted for the quantification of marine viruses belonging to a distinct virus family or group in field samples. It goes beyond counting "how many viruses in total" and provides precise information on "how many viruses of the particular clade of interest" are present in a given sample.

Project Overview

The traditional process of analyzing the ocean water samples using the Polony protocol is time-consuming, typically taking about 2.5 days for 20-30 samples. This process involves two main phases:

  1. Molecular Biology Work: This stage, which spans two days, is conducted in the laboratory. It involves molecular biology procedures to prepare samples for analysis. At the end of this stage for each sample 2 microscope slides containing a thin polyacrylamide gel with PCR amplicones labeled by fluorescence probes are performed.
  2. Polony Counting: After completing the molecular biology work, a set of high-resolution images of the gel are captured using a scanner. For each slide the set includes one RGB image and two black-and-white images representing the green and red channels, respectively. Those images of gel contain points named "polonies". Each point is a single phage amplicone labeled by fluorescence probe. Polonies appear in red, green, and yellow colors. They are counted and the number of polonies per slide is recalculated to the number of phages in the sample depanding on the Polony efficiency known for the studied gourp of viruses.

Our Goal

The primary objective of this project is to streamline and automate the Polony counting stage of the procedure. The aim is to reduce the amount of time that researchers spend on manual counting, which can be labor-intensive and time-consuming. The automation of counting will also help to standardize the process to eliminate the "human factor" from the final viruses concentrations meanings.

How to Use This Documentation

This documentation is structured to provide you with all the information needed to effectively use and contribute to the Polony Counter project. You'll find detailed tutorials, how-to guides, a comprehensive reference section, and thorough explanations of the underlying technology.

Below are links to pages in this documentation:

  1. Tutorials
  2. How-To Guides
  3. Reference
  4. Explanation

Contributions and Acknowledgments

We openly welcome contributions from developers, scientists, and researchers. Whether your expertise lies in image processing, machine learning, or molecular biology, your input can significantly enhance the capabilities of the Polony Counter.

I also extend my gratitude to Lindell's Lab at Technion, whose pioneering work in developing the original Polony protocol has been instrumental in the foundation of this project.