topostats 2.0.0

Automated Analysis for Atomic Force Microscopy Images of Biomolecules

TopoStats

| How to use | Installation | Tutorials and Examples | Contributing | Licence | Citation | |

An AFM image analysis program to batch process data and obtain statistics from images.

How to Use

There is more complete documentation on the projects documentation website. This is hosted in two locations.

• GitHub Pages : TopoStats
• Readthedocs : TopoStats

Installation

TopoStats is available via PyPI and can be installed in your Virtual Environment with...

pip install topostats

For more on installation please see the installation instructions

Tutorials and Examples

For a full description of usage please refer to the usage documentation.

A default configuration is loaded automatically and so the simplest method of processing images is to run run_topostats in the same directory as your scans after having activated the virtual environment in which you have installed TopoStats

run_topostats

If you have your own YAML configuration file (see Usage : Configuring TopoStats) then invoke run_topostats and use the argument for --config <config_file>.yaml that points to your file.

# Edit and save my_config.yaml then run TopoStats with this configuration file
run_topostats --config my_config.yaml

The configuration file is validated before analysis begins and if there are problems you will see errors messages that are hopefully useful in resolving the error(s) in your modified configuration.

Contributing

See contributing guidelines.

Licence

This software is licensed as specified by the GPL License and LGPL License.

Citation

• TopoStats – A program for automated tracing of biomolecules from AFM images