topostats
An AFM image analysis program to batch process data and obtain statistics from images
Science Score: 59.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 7 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org -
✓Committers with academic emails
9 of 18 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.3%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
An AFM image analysis program to batch process data and obtain statistics from images
Basic Info
- Host: GitHub
- Owner: AFM-SPM
- License: lgpl-3.0
- Language: Python
- Default Branch: main
- Homepage: https://afm-spm.github.io/TopoStats/
- Size: 998 MB
Statistics
- Stars: 75
- Watchers: 6
- Forks: 19
- Open Issues: 144
- Releases: 9
Topics
Metadata Files
README.md
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...
bash
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
bash
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.
```bash
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
Owner
- Name: Software for AFM & SPM data analysis
- Login: AFM-SPM
- Kind: organization
- Website: https://www.rms.org.uk/group/afm-spm.html
- Repositories: 4
- Profile: https://github.com/AFM-SPM
A community hub for Atomic Force Microscopy and Scanning Probe Microscopy analysis code
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| SylviaWhittle | s****e@g****m | 1,232 |
| Neil Shephard | n****d@s****k | 841 |
| Max Gamill | m****1@s****k | 801 |
| pre-commit-ci[bot] | 6****] | 159 |
| alicepyne | a****e@u****k | 131 |
| Robert (Bob) Turner | r****r@s****k | 115 |
| JoeBeton | j****n@h****k | 84 |
| Jean-Du | m****2@s****k | 66 |
| Laura Wiggins | l****s@s****k | 30 |
| derollins | d****1@g****m | 13 |
| TomC | t****y@s****k | 12 |
| slackline | n****d@p****m | 9 |
| bobturneruk | 3****k | 6 |
| Ben Thomas | b****s@s****k | 3 |
| dependabot[bot] | 4****] | 2 |
| Test | t****t@L****l | 1 |
| Daniel Eddie Rollins | d****1@s****k | 1 |
| ucapkah | 4****h | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 352
- Total pull requests: 498
- Average time to close issues: 6 months
- Average time to close pull requests: 14 days
- Total issue authors: 21
- Total pull request authors: 13
- Average comments per issue: 1.2
- Average comments per pull request: 1.57
- Merged pull requests: 388
- Bot issues: 1
- Bot pull requests: 52
Past Year
- Issues: 122
- Pull requests: 224
- Average time to close issues: 9 days
- Average time to close pull requests: 4 days
- Issue authors: 12
- Pull request authors: 10
- Average comments per issue: 0.5
- Average comments per pull request: 1.29
- Merged pull requests: 167
- Bot issues: 0
- Bot pull requests: 22
Top Authors
Issue Authors
- ns-rse (205)
- SylviaWhittle (58)
- MaxGamill-Sheffield (29)
- Jean-Du (17)
- derollins (14)
- llwiggins (4)
- tcatley (4)
- bobturneruk (3)
- LunchBobs (2)
- AdriSP2 (2)
- LHolmes2 (2)
- pre-commit-ci[bot] (1)
- Malisa-Vittoria (1)
- yetijbsmith (1)
- stavrina (1)
Pull Request Authors
- ns-rse (311)
- SylviaWhittle (80)
- MaxGamill-Sheffield (58)
- pre-commit-ci[bot] (49)
- llwiggins (11)
- dependabot[bot] (6)
- derollins (4)
- bobturneruk (3)
- iobataya (3)
- EvaMartinC (2)
- AuroVarat (2)
- tcatley (2)
- tobyallwood (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 165 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 8
- Total maintainers: 1
pypi.org: topostats
Automated Analysis for Atomic Force Microscopy Images of Biomolecules
- Documentation: https://AFM-SPM.github.io/TopoStats
- License: GNU Lesser GPLv3 only
-
Latest release: 2.3.1
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
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- actions/checkout v3 composite
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- codecov/codecov-action v3.1.1 composite
- h5py *
- igor *
- matplotlib *
- numpy ==1.23.4
- pandas *
- pySPM *
- pyfiglet *
- pyyaml *
- ruamel.yaml *
- schema *
- scikit-image *
- scipy *
- seaborn *
- tifffile *
- tqdm *