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PatchView

PatchView: A Python Package for Patch-clamp Data Analysis and Visualization - Published in JOSS (2022)

https://github.com/zeitgeberh/patchview

Science Score: 95.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ✓
    Committers with academic emails
    1 of 5 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

data-analysis data-visualization neuroscience patch-clamp-recordings

Scientific Fields

Mathematics Computer Science - 84% confidence
Last synced: 6 months ago · JSON representation

Repository

python toolkits and GUI for multi-patch whole-cell data analysis and visualization

Basic Info
Statistics
  • Stars: 22
  • Watchers: 4
  • Forks: 5
  • Open Issues: 0
  • Releases: 10
Topics
data-analysis data-visualization neuroscience patch-clamp-recordings
Created over 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct

README.rst 

===============
PatchView
===============
.. image:: https://img.shields.io/pypi/v/patchview.svg 
        :target: https://pypi.python.org/pypi/patchview
      
.. image:: https://img.shields.io/badge/python-3.10%2B-blue
        :target: https://www.python.org/downloads/release/python
        :alt: Python3.8

.. image:: https://readthedocs.org/projects/patchview/badge/?version=latest
        :target: https://patchview.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status

.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/psf/black

.. image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg
        :target: https://opensource.org/licenses/BSD-3-Clause
        :alt: BSD-3-Clause    

.. image:: https://joss.theoj.org/papers/10.21105/joss.04706/status.svg
   :target: https://doi.org/10.21105/joss.04706
.. image:: https://img.shields.io/pypi/dm/patchview?label=pypi%20downloads
           

.. image:: docs/resources/images/patchview_ads.png
    :width: 800

PatchView perform data analysis and visualization on multi channel whole-cell recording (multi-patch) data, including firing pattern analysis, event analysis,
synaptic connection detection, morphological analysis and more.

* Free software: BSD 3-Clause license
* Documentation: https://patchview.readthedocs.io.


Features
--------
PatchView integrates multiple open-source tools (see credit page) and wrap them using an intuitive graphic user interface (GUI).
Thus users can perform most analysis quickly for the data collected in a typical patch-clamp experiment without installing Python and 
these tools or writing any Python scripts.

* Importing both Heka data and Axon Instruments data (Both ABF1 and ABF2). Exporting to Python pickle file or NWB (Neurodata Without Borders) file format.
* Visualizing single and multiple traces with zoom, pan operations.
* Automatically sorting experiments data according to predefined labels.
* Performing analysis on intrinsic membrane properties, action potential detection, firing pattern analysis.
* Synaptic connection analysis.
* Visualizing and quantification of neuron's morphological reconstruction from Neurolucida

For Windows user
-----------------
Download zip file from `latest release `_. Unzip it, double click Patchview excutable file. 

To install PatchView from PyPI
---------------------------------
It is recommended to install Patchview in an virtual enviroment with Python3.10 (Python version >3.10 is not compatible with PySide2, which Patchview currently use)
After activating your virtual environment, run this command in your terminal:

.. code-block:: bash

        pip install git+https://github.com/ZeitgeberH/NeuroM@patchview#egg=NeuroM git+https://github.com/ZeitgeberH/dictdiffer#egg=dictdiffer git+https://github.com/jeremysanders/pyemf3#egg=pyemf3
        pip --no-cache-dir install patchview

More details or documentation for installation from source, please refer to the `Installation `_ page.

Citation
---------
If you find our work useful for your research, please cite:

    Hu et al., (2022). PatchView: A Python Package for Patch-clamp Data Analysis and Visualization. Journal of Open Source Software, 7(78), 4706, https://doi.org/10.21105/joss.04706

Owner

  • Name: Ming Hu
  • Login: ZeitgeberH
  • Kind: user
  • Location: Houston

| physics > < math | neuroscience>

JOSS Publication

PatchView: A Python Package for Patch-clamp Data Analysis and Visualization
Published
October 09, 2022
DOI
Volume 7, Issue 78, Page 4706
Authors
Ming Hu ORCID
Department of Neuroscience, Baylor College of Medicine, Houston, TX, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston,TX, USA
Xiaolong Jiang
Department of Neuroscience, Baylor College of Medicine, Houston, TX, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston,TX, USA, Department of Ophthalmology, Baylor College of Medicine, Houston, TX
Editor
Jacob Schreiber ORCID
Tags
neuroscience patch-clamp mini-event Heka Axon instruments
View PDF Review Thread Software Archive

GitHub Events

Total
  • Issues event: 4
  • Watch event: 5
  • Issue comment event: 4
  • Push event: 2
  • Fork event: 1
Last Year
  • Issues event: 4
  • Watch event: 5
  • Issue comment event: 4
  • Push event: 2
  • Fork event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 120
  • Total Committers: 5
  • Avg Commits per committer: 24.0
  • Development Distribution Score (DDS): 0.117
Past Year
  • Commits: 3
  • Committers: 2
  • Avg Commits per committer: 1.5
  • Development Distribution Score (DDS): 0.333
Top Committers
Name Email Commits
Zeta Z****H 106
Zeitgeber z****H@g****b 8
Hu u****7@b****u 3
Zeitgeber Z****H@g****b 2
Jan Freyberg j****g 1
Committer Domains (Top 20 + Academic)
bcm.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 17
  • Total pull requests: 4
  • Average time to close issues: 6 days
  • Average time to close pull requests: about 6 hours
  • Total issue authors: 8
  • Total pull request authors: 3
  • Average comments per issue: 2.76
  • Average comments per pull request: 0.25
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: 4 days
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mstimberg (7)
  • janfreyberg (3)
  • zf-basi77 (2)
  • tvajtay (1)
  • LouisonPineau (1)
  • marcel-goldschen-ohm (1)
  • bendichter (1)
Pull Request Authors
  • ZeitgeberH (4)
  • janfreyberg (1)
  • dependabot[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 74 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 13
  • Total maintainers: 1
pypi.org: patchview

Patchview perform data analysis and visualization on whole-cell recording data, including firing pattern analysis, event analysis, synatpic connection detection, morphorlocial analysis and more.

  • Versions: 13
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 74 Last month
Rankings
Dependent packages count: 6.6%
Average: 23.2%
Forks count: 23.2%
Dependent repos count: 30.6%
Stargazers count: 32.3%
Maintainers (1)
mlk99
Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi
  • furo *
requirements.txt pypi
  • Pillow *
  • PyOpenGL *
  • PyOpenGL_accelerate >=3.1.6
  • PySide2 *
  • colorcet *
  • cython *
  • future ==0.18.2
  • h5py ==3.7.0
  • joblib *
  • matplotlib *
  • neo *
  • numpy >=1.22,<1.24
  • pandas *
  • pyYAML ==6.0
  • pylru ==1.2.1
  • pynwb *
  • pyqt5 *
  • pyqt5-sip *
  • pyqtgraph *
  • pyqtwebengine *
  • python-dateutil *
  • pytz *
  • scikit-image *
  • scipy *
  • seaborn *
  • sklearn *
  • tqdm *
environment.yml pypi
  • Pillow *
  • PyOpenGL *
  • PyOpenGL_accelerate *
  • PyQT5 *
  • PySide2 *
  • colorcet *
  • cython *
  • future ==0.18.2
  • h5py ==3.7.0
  • joblib *
  • matplotlib *
  • neo *
  • numpy >=1.22,<1.24
  • pandas *
  • pyYAML ==6.0
  • pylru ==1.2.1
  • pyqtgraph *
  • pyqtwebengine *
  • scikit-image *
  • tqdm *
setup.py pypi