https://github.com/thennen/counting-molecules
Automates counting and categorization of molecules in scanning probe microscopy images
https://github.com/thennen/counting-molecules
cluster-analysis computer-vision image-analysis microscopy molecules zernike-moments
Last synced: 4 months ago
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Automates counting and categorization of molecules in scanning probe microscopy images
- Host: GitHub
- URL: https://github.com/thennen/counting-molecules
- Owner: thennen
- License: mit
- Created: 2018-07-16T15:09:10.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2024-09-02T08:06:48.000Z (almost 2 years ago)
- Last Synced: 2025-04-11T04:37:15.774Z (about 1 year ago)
- Topics: cluster-analysis, computer-vision, image-analysis, microscopy, molecules, zernike-moments
- Language: Python
- Homepage:
- Size: 1.62 MB
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# counting-molecules
[](https://zenodo.org/badge/latestdoi/141155345)
This project contains a set of functions to automate the counting and categorization of molecules, and is specifically tailored for data generated from low temperature scanning probe microscopes.
We described our approach in [Software Impacts](https://www.softwareimpacts.com/article/S2665-9638(22)00041-0/fulltext), and the code was also used to generate Fig. 3 of [this publication](https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201812334).
## Getting Started
This is a glorified script that makes use of existing python libraries. Written in python 3+, if unsure, start by installing [Anaconda](https://www.anaconda.com/download).
### Dependencies
* [Python 3+](https://www.anaconda.com/download)
* [SciPy](https://www.scipy.org/)
* [NumPy](http://www.numpy.org/)
* [Matplotlib](https://matplotlib.org/)
* [matplotlib-scalebar](https://pypi.org/project/matplotlib-scalebar/)
* [Scikit-image](https://scikit-image.org/)
* [Scikit-learn](https://scikit-learn.org/stable/)
* [Nanonispy](https://github.com/underchemist/nanonispy)
* [Mahotas](https://mahotas.readthedocs.io/en/latest/)
### Installing
This package is not yet registered. To install, clone this repository, navigate to its directory, and run:
```
pip install .
```
### Examples
`Helicene_example`, `APT_example` and `APT_2_example` are three example scripts that generate the figures in our [article](https://www.softwareimpacts.com/article/S2665-9638(22)00041-0/fulltext).
Steps to reproduce:
1. Download the data files from this [figshare repo](https://doi.org/10.6084/m9.figshare.19217556) into the examples folder.
2. Run the individual script files in the examples folder to generate each figure.
## Versioning
We use github, see the [tags on this repository](https://github.com/thennen/counting-molecules/tags)
## Authors
* **Jack Hellerstedt** [jhellerstedt](https://github.com/jhellerstedt)
* **Tyler Hennen** [THennen](https://github.com/thennen)
## License
This project is licensed under the MIT License.
## Acknowledgements
This project was inspired by the need to analyze the data that eventually resulted in [this publication](https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201812334).
We also made use of the data available from [this work.](https://www.nature.com/articles/nchem.2662)
This happened at the [Nanosurf lab.](https://nanosurf.fzu.cz/)