TopoStats

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

There is more complete documentation on the projects documentation website.

Installation

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

pip install topostats

For more on installation and how to upgrade please see the installation instructions.

NB The minimum supported version of Python is >=3.10 and because of a constraint in a dependency the maximum supported version is <= 3.11 (for now, we hope to support newer versions in the near future).

How to Use

Tutorials and Examples

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

A default configuration is loaded automatically that works with .spm files. The simplest method of processing images is to run topostats process in the same directory as your scans after having activated the virtual environment in which you have installed TopoStats

topostats process

If you have files other than .spm please refer topostats --help and the documentation on how to process those images with TopoStats.

NB If your configuration specifies .spm (the default) files with the old-style Bruker extension (i.e. .001, .002 etc.) will also be processed.

If you have your own YAML configuration file (see Usage : Configuring TopoStats) then invoke topostats and use the argument for --config <config_file>.yaml that points to your file with an associated module of TopoStats e.g. process.

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

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.

You can generate a sample configuration file using the topostats create-config argument which writes the default configuration to the file ./config.yaml (i.e. in the current directory). This will not run any analyses.

Notebooks

Example Jupyter Notebooks have been developed that show how to use TopoStats package interactively which is useful when you are unsure of what parameters are most suited to your scans. Other notebooks exist which show how to produce plots of the summary grain and tracing statistics or how to generate plots of scans from processed images which saves having to run the processing again. See the documentation on Notebooks for further details.

Contributing

Please refer to our contributing guidelines documentation.

Licence

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

Citation

If you use TopoStats in your work or research please cite us. There is a Citation File Format in this repository to aid citation.

Publications

• TopoStats - Atomic Force Microscopy image processing and analysis doi:10.15131/shef.data.22633528.v2
• Pre-Print Under or Over? Tracing Complex DNA Structures with High Resolution Atomic Force Microscopy | bioRxiv doi:10.1101/2024.06.28.601212