Data

Tools

Indexes

Applications

Experiments

Open Source Science

PyView

PyView: A general purpose tool for analyzing calcium imaging data - Published in JOSS (2023)

https://github.com/galizia-lab/pyview

Science Score: 98.0%

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
    2 of 4 committers (50.0%) from academic institutions
  • ✓
    Institutional organization owner
    Organization galizia-lab has institutional domain (neuro.uni-konstanz.de)
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

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

Repository

GUI + API for processing and visualizing Calcium imaging data. Largely based on the IDL software "VIEW" developed by Giovanni Galizia. Implemented in Python by Ajayrama Kumaraswamy

Basic Info
  • Host: GitHub
  • Owner: galizia-lab
  • License: bsd-3-clause
  • Language: Jupyter Notebook
  • Default Branch: master
  • Size: 47.9 MB
Statistics
  • Stars: 6
  • Watchers: 2
  • Forks: 3
  • Open Issues: 8
  • Releases: 4
Created over 4 years ago · Last pushed 7 months ago
Metadata Files
Readme License

README.md

Welcome to the repository containing the python implementation of PyView

PyView is a general purpose tool to analyze calcium imaging data of responses to sensory stimuli.

It provides a powerful GUI to interactively visualize, analyse and assess the quality of imaging stacks; and flexibly select steps and parameters for removing artifacts and for estimating neural activity levels. The GUI is based on the core functions and classes of PyView that can be used for identical batch processing, i.e. running all experimental measurements through the processing steps selected above using one single set of parameters to produce time traces, 2D images or 3D movies

Getting started

Installation

Quick guide

(assuming you have anaconda installed) - create a conda environment using condapy310linux.yml or condapy310mac_win.yml - Take note tag of the latest release of PyView from here. - Install PyView using pip install git+https://git@github.com/galizia-lab/pyview.git@<tag name>

Detailed guides

Please consult this page on our wiki for detailed guides on installation and updating as normal users and as developers.

Starting PyView-GUI

  1. Open a terminal/Powershell and activate the environment created for PyView). For example conda activate view_py310
  2. Try launching PyView with the command "view".

Tutorial

A quick hands-on tour of the GUI and batch processing capabilities of PyView is provided by this section of the wiki, using a synthetic dataset. Before you begin, make sure to copy the folder "synthetic_data" into a place of your system where you keep data. (If you installed as a developer, the folder is part of the your local clone of the source code of PyView. If you installed as a simple user, get a ZIP or TARBALL of the source code of the lastest release of PyView here).

More Resources and documentation

License

BSD 3 Clause, see file LICENSE-BSD-3-CLAUSE

Issues

If you find bugs, have questions about its usage, or have ideas for new features, please check the Issues tab first for related Issues before creating a new issue. For bugs and errors, please paste the error you have encountered, mention your operating system and clearly state the steps to reproduce the error. Attach sample data if it is needed to reproduce the error. Thank You!

Contributing

Please consult this page on the wiki for a Developer Guide. Pull requests corresponding to well documented issues in this repository are welcome!

Citing

Please consider citing our JOSS paper if PyView was useful for your research, investigations or other intellectual work.

Owner

  • Name: Galizia Lab
  • Login: galizia-lab
  • Kind: organization
  • Location: Germany

We research insect olfaction at the University of Konstanz, Germany

JOSS Publication

PyView: A general purpose tool for analyzing calcium imaging data
Published
February 21, 2023
DOI
Volume 8, Issue 82, Page 4936
Authors
Ajayrama Kumaraswamy ORCID
University of Konstanz, Department of Biology, Universitatsstr. 10, D-78457 Konstanz
Georg Raiser ORCID
Champalimaud Centre for the Unknown, Avenida de Brasília, 1400-038 Lisboa, Portugal
C Giovanni Galizia ORCID
University of Konstanz, Department of Biology, Universitatsstr. 10, D-78457 Konstanz
Editor
Charlotte Soneson ORCID
Tags
Neuroscience Calcium imaging
View PDF Review Thread Software Archive

GitHub Events

Total
  • Issues event: 2
  • Delete event: 1
  • Issue comment event: 4
  • Push event: 4
  • Pull request event: 2
  • Create event: 2
Last Year
  • Issues event: 2
  • Delete event: 1
  • Issue comment event: 4
  • Push event: 5
  • Pull request event: 2
  • Create event: 2

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 65
  • Total Committers: 4
  • Avg Commits per committer: 16.25
  • Development Distribution Score (DDS): 0.477
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Giovanni Galizia g****a@u****n 34
Ajayrama Kumaraswamy a****y@t****m 28
Ajayrama Kumaraswamy a****y@u****e 2
galizia g****a@u****e 1
Committer Domains (Top 20 + Academic)
uni-konstanz.de: 2 tutamail.com: 1 uni.kn: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 20
  • Total pull requests: 22
  • Average time to close issues: 4 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 5
  • Total pull request authors: 3
  • Average comments per issue: 1.25
  • Average comments per pull request: 0.23
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: about 2 months
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.25
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • adamltyson (8)
  • galizia (5)
  • ajkswamy (3)
  • Yannan-Chen (3)
  • IngaPetelski (1)
Pull Request Authors
  • ajkswamy (16)
  • galizia (4)
  • csoneson (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

setup.py pypi
  • Pillow >=6.0.0
  • See *
  • Source *
  • appdirs >=1.4.3
  • bokeh >=2.0.0
  • easygui >=0.98.1
  • gekko >=0.2.8
  • iltis *
  • itables >=0.2.1
  • jinja2 >=2.10.3
  • matplotlib >=3.0.3
  • moviepy >=1.0.0
  • neo >=0.9.0
  • numpy >=1.16.3
  • openpyxl >=3.0.3
  • pandas >=0.24.2
  • pyyaml >=3.3
  • quantities >=0.12.4
  • scikit-image >=0.15.0
  • scipy *
  • seaborn >=0.10.0
  • textfsm >=1.1.0
  • tifffile >=2019.7.26
  • tillvisionio *
  • whoosh >=2.7.4