CHIPS: an Extensible Toolbox for Cellular and Hemodynamic Two-Photon Image Analysis
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Two-photon microscopy is able to produce exquisite and informative functional images of cells and blood vessels in living animals or tissue,1 especially when combined with genetically-encoded indicators of cellular activity.2 Since these imaging techniques typically produce too much data to analyse manually, a number of automated or semi-automated image analysis approaches have been developed. However, even aside from the algorithms themselves, many factors can complicate analysis workflows.
For example: 1) it can be tedious to extract and format the metadata required by the algorithm from the raw images; 2) users may want to perform one or more pre-processing steps, such as motion correction or spectral unmixing, before starting the primary analysis; 3) even when code is available for a published algorithm, it may not be supplied in a form that can be executed easily by users with limited programming experience, and it may not run on different platforms or in different software...
The authors are grateful to the many colleagues and collaborators who have provided feedback, suggestions and testing during the development process; to Rachel Barrett for assistance with documentation; and to the many developers who have made versions of their code and/or algorithms available. MJPB and JLS received funding from the University of Zurich Forschungskredit. JLS received funding from the Heart and Stroke Foundation of Canada. BW is a member of the University of Zurich Clinical Research Priority Program on Molecular Imaging.
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Conflict of Interest
The authors declare that they have no conflict of interest.