AFMReader

A Napari plugin to read in Atomic Force Microscopy (AFM) files using AFMReader.

You can drag and drop your favourite AFM image files directly into the Napari viewer to use the awesome tools the image analysis community have developed over at the Napari Hub to analyse your images using open-source software and a GUI!

File Extension	Supported by AFMReader	Description
.asd	✅	High-speed AFM format.
.gwy	✅	Gwyddion saved format.
.ibw	✅	Igor binary-wave format.
.jpk	✅	JPK instruments format.
.spm	✅	Bruker spm format.
.stp	✅	Homemade stp format.
.top	✅	Homemade top format.
.topostats	✅	topostats output format.

Installation¶

Via Napari-Hub¶

This software should be installable directly from Napari!

All you need to do is:

1. Install Napari into an environment.

2. Open Napari by typing napari into your command line with your Napari environment activated.

   napari

3. Go to Plugins > Install/Uninstall Plugins, and search for napari-afmreader.

Via Git¶

Occasionally the Napari-Hub version of napari-AFMReader may not be the most up-to-date. This is when you might want to install both the most up-to-date AFMReader and napari-AFMReader versions via Git.

napari-AFMReader has been designed to need minimal maintenance, with most of the new file type additions being solely added to AFMReader.

1. With Git installed on your machine, clone both the AFMReader and napari-AFMReader repositories:

   git clone https://github.com/AFM-SPM/AFMReader.git

   git clone https://github.com/AFM-SPM/napari-AFMReader.git

2. Activate your Python environment (e.g. Conda) and install the dependencies for each - make sure that the AFMReader dependency is installed second to overwrite the possibly outdated afmreader package!

   cd napari-AFMReader
   pip install .
   cd ..

   cd AFMReader
   pip install .

3. Now when you open Napari via the napari command, it should use the latest version of AFMReader, and napari-AFMReader.

   napari

Usage¶

This package should be fairly straight-forward and intuitive to use, requiring you to:

1. Drag and drop your supported AFM file into the Napari Viewer.

2. Type in the name of the channel you would like to use. You may not need to specify a channel for e.g. .stp, or the channel may refer to image key in the .napari-afmreader file.*.

   *Possible channel names will not appear at first due to the order in which AFMReader processes an image. Thus, when provided with an non-existent channel name, the dialogue box will then return a list of possible channels to choose from.

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.