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Welcome to the repository containing PyView, the python implementation of VIEW

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 conda_py310_linux.yml or conda_py310_mac_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

Open a terminal/Powershell and activate the environment created for PyView). For example conda activate view_py310
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).

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.

datacite.yml
Title	PyView: A general purpose tool for analyzing calcium imaging data
Authors	Kumaraswamy,Ajayrama;Universität Konstanz, Konstanz, Germany;ORCID:0000-0001-7928-877X Raiser,Georg;Champalimaud Centre for the Unknown, Avenida de Brasília, 1400-038 Lisboa, Portugal;ORCID:0000-0002-9716-3513 Galizia,C. Giovanni;Universität Konstanz, Konstanz, Germany;ORCID:0000-0001-8292-6031
Description	Welcome to the archived version of the repository containing PyView, the python implementation of View! 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
License	3-Clause BSD License (https://opensource.org/licenses/BSD-3-Clause)
References	Kumaraswamy A, Raiser G, Galizia CG (2023). PyView: A general purpose tool for analyzing calcium imaging data. Journal of Open Source Software, 8(82), 4936, https://doi.org/10.21105/joss.04936 [doi:10.21105/joss.04936] (IsSupplementTo) Kumaraswamy A, Galizia CG (2022) Collection of Datasets for testing PyVIEW. G-Node. https://doi.org/10.12751/g-node.4c44i5 [doi:10.12751/g-node.4c44i5] (References)
Funding	Federal Ministry of Education and Research (BMBF) as part of the Excellence Strategy of the German Federal and State Governments Baden-Württemberg Ministry of Science as part of the Excellence Strategy of the German Federal and State Governments
Keywords	Neuroscience Python Calcium imaging
Resource Type	Software

README.md