TopoStats

| Installation | Tutorials and Examples | Contributing | Licence | Citation |

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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.

How to Use

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 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 your own YAML configuration file (see Usage : Configuring TopoStats) then invoke topostats process 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
topostats process --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.

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.

NB - This feature is only available in versions > v2.0.0 as it was introduced after v2.0.0 was released. In older version > 2.0.0 and <= 2.1.2 you can use the older run_topostats --create-config option.

run_topostats --create-config-file config.yaml

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

See contributing guidelines.

Licence

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

Citation

Please use the Citation File Format which is available in this repository.

Publications

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