vodex 1.0.11

VoDEx : Volumetric Data and Experiment Manager. Allows to load volumetric data based on experimental conditions.

VoDEx: Volumetric Data and Experiment manager

A python library to load volumetric data based on experimental conditions.

Installation

You can install vodex via pip:

pip install vodex

Documentation

To get started with vodex, please refer to the Documentation.

About

Recent advances in fluorescent microscopy and genetically-encoded calcium indicators made it possible to acquire large-scale 3D-time series datasets of brain activity. During these recordings, experimental conditions can vary: subjects can be presented with different stimuli and/or demonstrate different behavior. It is then required to annotate the data based on these experimental conditions and select the recording time of interest for the subsequent analysis. Data annotation is usually done manually or using a custom code deeply integrated with the analysis pipeline. Manual annotation is prone to error and is hard to document. Custom code often requires loading the whole dataset into the memory or depends on the exact file representation of data on a disc, which is not optimal for large datasets.

We introduce VoDEx, volumetric data and experiment manager, a data management tool that integrates the information about the individual image frames, volumes, volume slices, and experimental conditions and allows retrieval of sub-portions of the 3D-time series datasets based on any of these identifiers. It is implemented as a napari plugin for interactive usage with a GUI and as an open-source Python package for easy inclusion into analysis pipelines.

Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the [BSD-3] license, vodex is free and open source software