Imaging+¶
Welcome to the imaging+ documentation!¶
This documentation contains guides and information about the usage and structure of imaging+.
Please follow the instructions for installation and provided guides to get you started with utilizing the package.
Please open an issue or pull request on the project’s Github page if you are encountering any problems with the package.
Introduction¶
imaging+ is an integrated tool-suite for essential processing, analysis and data visualization steps for multimodal calcium imaging+ neuroscience experiments in Python.
This tool-suite was first designed to serve as a scalable data analysis framework for all-optical experiments that combine 2-photon imaging, 2-photon optogenetic stimulation and multiple time-synced data signals (Packer et al., 2015, Nat Methods).
The imaging+ framework is more broadly useful for multi-modal imaging+ neuroscience experiments, in which calcium imaging data is collected with other time-synchronized signals.
Especially, there are methods for analysis and visualisation of standard calcium imaging data.
Currently, imaging+ is most functional for experiments performed using PackIO for temporal synchronization, a Bruker microscope for 2p imaging and utilizing Suite2p for automated post-processing cell segmentation.
imaging+ integrates the AnnData framework for native and highly efficient, HDF-5 compatible storage and organization of all levels of the data analysis workflow from preprocessing to highly analyzed downstream forms as well.
Follow installation for installation. Please refer to Quick Start Guide, Tutorials and Core structures to get started and learn the toolbox.