SyMBac Documentation

SyMBac (Synthetic Micrographs of Bacteria) is a tool to generate synthetic phase contrast or fluorescence images of bacteria. Currently the tool only supports bacteria growing in the mother machine and on agar pads.

Coming soon:

• Agar pad simulations (working, code being added)

• Command line interface (currently testing)

Read the preprint, SyMBac: Synthetic Micrographs for Accurate Segmentation of Bacterial Cells using Deep Neural Networks, Georgeos Hardo, Maximillian Noka, Somenath Bakshi

Note

This project is under active development. Please report issues on GitHub, or if you want specific usage help, please email me.

Contents

Introduction

• Introduction
  • What is it?
  • Why would I want to generate synthetic images?
  • How do I use these synthetic images?
• Installation
  • Prerequisites
  • Installation
    • If you’re using a GPU
    • If you aren’t using a GPU
• FAQs

Guide: Mother Machine

• Mother machine simulations
  • Running a simulation
  • Simulation visualisation
  • Point spread function (PSF) generation
  • Camera model
  • Rendering

Guide: Agar Pad

• Agar pad simulations
  • This notebook is currently being updated, and is unfinished!

Examples

• Convert SyMBac data to be compatible with Omnipose
• Training Omnipose
• Segmenting with Omnipose

Classes reference

• SyMBac.cell
• SyMBac.PSF
• SyMBac.renderer
• SyMBac.simulation

API reference

• SyMBac.cell_geometry
• SyMBac.cell_simulation
• SyMBac.drawing
• SyMBac.misc
• SyMBac.pySHINE