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napari-afmreader

A Napari plugin to read in AFM files via AFMReader.

https://github.com/afm-spm/napari-afmreader

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
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    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

A Napari plugin to read in AFM files via AFMReader.

Basic Info
  • Host: GitHub
  • Owner: AFM-SPM
  • License: gpl-3.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 55.6 MB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 2
  • Releases: 2
Created 10 months ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

napari-AFMReader

[![PyPI version](https://badge.fury.io/py/napari-afmreader.svg)](https://badge.fury.io/py/napari-afmreader) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/napari-afmreader) [![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Code style: flake8](https://img.shields.io/badge/code%20style-flake8-456789.svg)](https://github.com/psf/flake8) [![codecov](https://codecov.io/gh/AFM-SPM/napari-afmreader/branch/dev/graph/badge.svg)](https://codecov.io/gh/AFM-SPM/napari-afmreader) [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/AFM-SPM/napari-afmreader/main.svg)](https://results.pre-commit.ci/latest/github/AFM-SPM/napari-afmreader/main) [![ORDA](https://img.shields.io/badge/ORDA--DOI-10.15131/shef.data.29263577.v.1-lightgrey)](https://figshare.shef.ac.uk/articles/software/napar-AFMReader/) [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B-yellow)](https://fair-software.eu)
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| [Installation](#installation) | [Usage](#usage) | [Licence](#licence) | [Citation](#citation) |

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.

bash napari

  1. 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:

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

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

  1. 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!

bash cd napari-AFMReader pip install . cd ..

bash cd AFMReader pip install .

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

bash 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.

Owner

  • Name: Software for AFM & SPM data analysis
  • Login: AFM-SPM
  • Kind: organization

A community hub for Atomic Force Microscopy and Scanning Probe Microscopy analysis code

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: napari-AFMReader
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Max
    family-names: Gamill
    email: mcgamill1@sheffield.ac.uk
    affiliation: The University of Sheffield
    orcid: "https://orcid.org/0009-0007-3250-5299"
  - given-names: Neil
    family-names: Shephard
    email: n.shephard@sheffield.ac.uk
    affiliation: The University of Sheffield
    orcid: "https://orcid.org/0000-0001-8301-6857"
  - given-names: Syliva
    family-names: Whittle
    email: sylvia.whittle@sheffield.ac.uk
    affiliation: The University of Sheffield
    orcid: "https://orcid.org/0009-0008-9164-9513"
  - given-names: Alice
    family-names: Pyne
    email: a.l.pyne@sheffield.ac.uk
    affiliation: The University of Sheffield
    orcid: "https://orcid.org/0000-0002-2658-8987"

identifiers:
  - type: url
    value: "https://github.com/AFM-SPM/napari-AFMReader.git"
    description: source code
  - type: doi
    value: 10.15131/shef.data.29263577
abstract: >-
  napari-AFMReader is Napari plugin to read Atomic Force Microscopy images.
keywords:
  - atomic force microscopy
  - python
  - napari
  - plugin
license: GPL-3.0
commit: cd0ec35a5071deb7f6f8ef6dce6598a542cb059b
version: 0.0.1
date-released: "2023-05-18"

GitHub Events

Total
  • Create event: 7
  • Issues event: 2
  • Release event: 3
  • Watch event: 1
  • Delete event: 4
  • Issue comment event: 3
  • Push event: 11
  • Pull request event: 11
Last Year
  • Create event: 7
  • Issues event: 2
  • Release event: 3
  • Watch event: 1
  • Delete event: 4
  • Issue comment event: 3
  • Push event: 11
  • Pull request event: 11

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 3
  • Total pull requests: 21
  • Average time to close issues: 21 days
  • Average time to close pull requests: 8 days
  • Total issue authors: 1
  • Total pull request authors: 5
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.1
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 5
Past Year
  • Issues: 3
  • Pull requests: 21
  • Average time to close issues: 21 days
  • Average time to close pull requests: 8 days
  • Issue authors: 1
  • Pull request authors: 5
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.1
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 5
View more stats
Top Authors
Issue Authors
  • ns-rse (3)
Pull Request Authors
  • ns-rse (10)
  • pre-commit-ci[bot] (4)
  • MaxGamill-Sheffield (4)
  • webknjaz (2)
  • dependabot[bot] (1)
Top Labels
Issue Labels
ci (2)
Pull Request Labels
dependencies (1) github_actions (1) ci (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 24 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
pypi.org: napari-afmreader

Napari plugin using AFMReader to load various Atomic Force Microscopy Images.

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 24 Last month
Rankings
Dependent packages count: 9.0%
Forks count: 24.2%
Average: 31.3%
Stargazers count: 41.3%
Dependent repos count: 50.8%
Maintainers (1)
topostats
Last synced: 6 months ago

Dependencies

.github/workflows/pypi.yaml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/test-pypi.yaml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/tests.yaml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • codecov/codecov-action v5 composite
  • mxschmitt/action-tmate v3 composite
pyproject.toml pypi
  • afmreader *
  • magicgui *
  • napari [all]
  • qtpy *
  • tox *