Welcome to the FlickerPrint documentation!

FlickerPrint is a Python package for determining the interfacial tension and bending ridgidity (as well as other properties) of a population of soft bodies such as condensates or vesicles by analysing their shape fluctuations in confocal microscopy images. This flicker spectroscopy analysis can be parallised across multiple cores to allow whole populations of soft bodies to be analysed.

Contents:

• User Guide
  • Installation
  • Getting started
  • Worked Example
• Details
  • Workflow
  • Image Requirements
  • Structure of the Experiment Directory
  • Configuration File
  • Data Storage

• Module Source Code

• Find Out More
  • FlickerPrint Papers
  • Contributors
  • Funding

Flicker Spectroscopy

Flicker spectroscopy is a method to measure the properties of biomolecular condensates by measuring the thermal fluctuations of their boundary (measuring the properties of vesicles is also supported). See the paper for more information about the theory used.

Quick Install

See Installation for details of the prerequesites for the package. Download the source code from GitHub, navigate to the FlickerPrint/src folder and install using pip:

Windows

python -m pip install .

macOS and Linux

python3 -m pip install .

Recording Images

FlickerPrint requires the use of confocal microscopy images, taken at (approximately) the equator of the objects of interest. Systems can be either in vitro or in live cells, provided that the condensates are in thermal equilibrium so are not being impacted by external forces or energies and that the objects display shape fluctuations above the resolution limit of FlickerPrint (typically \(\approx\) 0.1 pixels).

See Image Requirements for a guide to take images best suited for analysis.

Run Analysis

The package can be run from the command-line. Create an experiment directory with

flickerprint create-project EXPERIMENT_NAME

and run the analysis from that directory with

flickerprint run

See Getting started for a short guide or Workflow for more details.

Index and Search

• Index

• Module Index

• Search Page