PWSpy
PWSpy: A Python library dedicated to the analysis of Partial Wave Spectroscopic Microscopy data. - Published in JOSS (2022)
Science Score: 95.0%
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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 2 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: ncbi.nlm.nih.gov, nature.com, joss.theoj.org, zenodo.org -
✓Committers with academic emails
2 of 4 committers (50.0%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Scientific Fields
Repository
A Python library dedicated to the analysis of Partial Wave Microscopy (PWS) data.
Basic Info
- Host: GitHub
- Owner: BackmanLab
- License: gpl-3.0
- Language: Python
- Default Branch: master
- Size: 202 MB
Statistics
- Stars: 4
- Watchers: 1
- Forks: 3
- Open Issues: 1
- Releases: 19
Metadata Files
README.md
PWSpy
A Python module dedicated to analysis of Partial Wave Spectroscopic Microscopy data. Read the paper here
Statement of need
Any analysis of raw data generated by PWS and related imaging modes requires loading image data and metadata from a large variety of file formats, performing complex pre-processing steps before any of the real analysis begins. Any minor variations in how this pre-processing is performed can result in major differences in final analysis results. PWSpy provides an object-oriented interface for performing all common file I/O and analysis tasks related to PWS. This allows users to write succinct and readable scripts/software that function identically regardless of the file format of the raw data and which are guaranteed to perform all basic operations properly. The analysis steps described in previous publications (1, 2, 3) can be found written out clearly in Python under the analysis package. Classes providing uniform file handling for the current file format used by the PWS Acquisition plugin for Micro-Manager as well as all known legacy formats can be found under the dataTypes package. This library provides support for the backend code of PWSpy_GUI.
Documentation
API documentation is hosted online at ReadTheDocs
Installation
PWSpy is most easily installed with the Conda package manager.
It is advisable to install PWSpy into it's own Conda environment to avoid dependency conflicts.
Create a new environment with the command: conda create -n {environmentName} python=3.7. You can then make the new environment active in your terminal with conda activate {environmentName}.
More information here.
Installing from Anaconda Cloud (recommended)
PWSpy is published online to the "backmanlab" Anaconda Cloud channel. It can be installed from Conda with the command conda install -c conda-forge -c backmanlab pwspy
Installing with Pip
PWSpy is available on PyPi and can be installed using Pip, however some of its dependencies may not automatically install properly. Installing via conda is the easiest method.
Building from source and distributing
For information on creating a Conda package yourself see here.
Testing
Automated tests using the pytest framework reside under the tests directory. The default configuration for pytest can be found in pyproject.toml. Pytest 6.0 or greater is required. For more information on running pytest from the commandline or IDE integration please see the pytest documentation. The tests require that you first install the test dataset under tests/resources. Due to the size of the test dataset it is hosted externally rather than being included in the Git repository. Please check here for up to date information on how to acquire the test dataset.
Contributing
Read the contributing section in the documentation if you want to help us improve and further develop PWSpy!
Owner
- Name: Backman Lab
- Login: BackmanLab
- Kind: organization
- Location: United States of America
- Repositories: 2
- Profile: https://github.com/BackmanLab
JOSS Publication
PWSpy: A Python library dedicated to the analysis of Partial Wave Spectroscopic Microscopy data.
Authors
Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA.
Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA.
Editor
Jeff Gostick
Tags
Microscopy Hyperspectral ImagingCodeMeta (codemeta.json)
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"author": [
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"@id": "0000-0003-2882-2471",
"@type": "Person",
"email": "nicholas.anthony@northwestern.edu",
"name": "Nicholas M. Anthony",
"affiliation": "Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA."
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"identifier": "",
"codeRepository": "https://github.com/nanthony21/PWSpy",
"datePublished": "2021-11-09",
"dateModified": "2021-11-09",
"dateCreated": "2021-11-09",
"description": "A Python library dedicated to the analysis of Partial Wave Spectroscopic Microscopy data.",
"keywords": "Python, Microscopy, Hyperspectral Imaging",
"license": "GPS v3.0",
"title": "PWSpy",
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}GitHub Events
Total
Last Year
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Nick Anthony | n****y@n****u | 1,962 |
| Nick | n****y@h****m | 222 |
| Kyle Niemeyer | k****r@f****m | 1 |
| nai5790 | n****6@u****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 5
- Total pull requests: 18
- Average time to close issues: 6 days
- Average time to close pull requests: about 12 hours
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 3.6
- Average comments per pull request: 0.0
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- pr4deepr (3)
- hamsamilton (2)
Pull Request Authors
- nanthony21 (17)
- kyleniemeyer (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 242 last-month
- Total dependent packages: 1
- Total dependent repositories: 1
- Total versions: 18
- Total maintainers: 1
pypi.org: pwspy
A framework for working with Partial Wave Spectroscopic microscopy files.
- Homepage: https://github.com/BackmanLab/PWSpy
- Documentation: https://pwspy.readthedocs.io/
- License: gpl-3.0
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Latest release: 1.0.3
published about 2 years ago
Rankings
Maintainers (1)
Dependencies
- h5py *
- jsonschema *
- matplotlib *
- numpy *
- opencv-python *
- pandas *
- psutil *
- rasterio *
- scikit-image *
- scipy *
- shapely *
- tifffile *
- setuptools_scm *
- sphinx-autodoc-typehints *
- sphinx_rtd_theme *
- actions/checkout v2 composite
- actions/upload-artifact v1 composite
- openjournals/openjournals-draft-action v.1.0 composite
- actions/checkout v2 composite
- conda-incubator/setup-miniconda v2 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite