Ajayrama Kumaraswamy
ec87d78ffe
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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
(assuming you have anaconda installed)
pip install git+https://git@github.com/galizia-lab/pyview.git@<tag name>Please consult this page on our wiki for detailed guides on installation and updating as normal users and as developers.
conda activate view_py310A 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).
Kumaraswamy A., Raiser G., Galizia C. G. (2023). PyView: A general purpose tool for analyzing calcium imaging data. Journal of Open Source Software.
BSD 3 Clause, see file LICENSE-BSD-3-CLAUSE
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!
Please consult this page on the wiki for a Developer Guide. Pull requests corresponding to well documented issues in this repository are welcome!
Please consider citing our JOSS paper if PyView was useful for your research, investigations or other intellectual work.
| datacite.yml | |
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| 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 |