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Usage

There are two different ways of using AFMSlicer to process images, the Command Line Interface (CLI) which allows for batch processing of multiple images in parallel or a Graphical User Interface (GUI) built in Napari. This page describes how to use the command line version of AFMSlicer, for details of using the Napari GUI see the Napari page.

Data

You should place your raw AFM images as exported from the scanning machine in a directory to be processed where the Virtual Environment will be activated. If you have installed AFMSlicer from GitHub this will be the AFMSlicer you have cloned the repository to. If you have installed from PyPI this will be whatever directory you created to setup a Virtual Environment in.

Note

This isn't actually essential as you can either use the afmslicer --base-dir flag to specify an alternative directory to scan for images or modify ~base_dir: ./~ option in a custom configuration.

To keep data organised it is recommended to place it in the data/raw directory, optionally data from specific days or experiments may be grouped into sub-directories within these. AFMSlicer will automatically find all files with the user specified extension (which defaults to .spm).

.
└──   ./data
    └──   ./data/raw
        ├──   ./data/raw/e_coli
        │   ├──   ./data/raw/e_coli/20260303
        │   ├──   ./data/raw/e_coli/20260304
        │   └──   ./data/raw/e_coli/20260306
        └──   ./data/raw/staph
            ├──   ./data/raw/staph/20260320
            ├──   ./data/raw/staph/20260321
            ├──   ./data/raw/staph/20260323
            └──   ./data/raw/staph/20260326

Warning

If you edit your .spm file(s) in other software (e.g. Gwyddion) and then save them with the same file extension they may not load successfully with AFMSlicer.

If a file is edited in Gwyddion it should be saved in the native .gwy format as .tiff is not supported by AFMReader. For more information please refer to the relevant issue in AFMReader and the linked thread in the Gwyddion.

Once you have your data in an organised structure you can proceed to processing using either...