VoDEx: a Python library for time annotation and management of volumetric functional imaging data Article Swipe
Anna Nadtochiy
,
Peter Luu
,
Scott E. Fraser
,
Thai V. Truong
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btad568
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btad568
Summary In functional imaging studies, accurately synchronizing the time course of experimental manipulations and stimulus presentations with resulting imaging data is crucial for analysis. Current software tools lack such functionality, requiring manual processing of the experimental and imaging data, which is error-prone and potentially non-reproducible. We present VoDEx, an open-source Python library that streamlines the data management and analysis of functional imaging data. VoDEx synchronizes the experimental timeline and events (e.g. presented stimuli, recorded behavior) with imaging data. VoDEx provides tools for logging and storing the timeline annotation, and enables retrieval of imaging data based on specific time-based and manipulation-based experimental conditions. Availability and implementation VoDEx is an open-source Python library and can be installed via the “pip install” command. It is released under a BSD license, and its source code is publicly accessible on GitHub (https://github.com/LemonJust/vodex). A graphical interface is available as a napari-vodex plugin, which can be installed through the napari plugins menu or using “pip install.” The source code for the napari plugin is available on GitHub (https://github.com/LemonJust/napari-vodex). The software version at the time of submission is archived at Zenodo (version v1.0.18, https://zenodo.org/record/8061531).
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/bioinformatics/btad568
- https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad568/51529667/btad568.pdf
- OA Status
- gold
- Cited By
- 1
- References
- 26
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4377565316
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4377565316Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/bioinformatics/btad568Digital Object Identifier
- Title
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VoDEx: a Python library for time annotation and management of volumetric functional imaging dataWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2023Year of publication
- Publication date
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2023-09-01Full publication date if available
- Authors
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Anna Nadtochiy, Peter Luu, Scott E. Fraser, Thai V. TruongList of authors in order
- Landing page
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https://doi.org/10.1093/bioinformatics/btad568Publisher landing page
- PDF URL
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https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad568/51529667/btad568.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
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https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad568/51529667/btad568.pdfDirect OA link when available
- Concepts
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Python (programming language), Plug-in, Computer science, Timeline, MIT License, Source code, Software, Open source, Annotation, Information retrieval, Database, Programming language, Artificial intelligence, Archaeology, HistoryTop concepts (fields/topics) attached by OpenAlex
- Cited by
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1Total citation count in OpenAlex
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2024: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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