CHIPS: an Extensible Toolbox for Cellular and Hemodynamic Two-Photon Image Analysis
Two-photon microscopy is able to produce exquisite and informative functional images of cells and blood vessels in living animals or tissue, especially when combined with genetically-encoded indicators of cellular activity. 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 versions; 4) users may want to run different algorithms for the same type of analysis (e.g. for measuring activity in different cell types), but not maintain multiple disparate processing pipelines; 5) the process of optimising analysis parameters, plotting, and data output can be tedious; and 6) processing groups of similar images may be difficult or inefficient. With these factors in mind, we developed CHIPS (Cellular and Hemodynamic Image Processing Suite), an open-source toolbox, to streamline image analysis pipelines. CHIPS integrates a number of algorithms, both novel and existing, into a complete image processing pipeline, and is applicable to a range of cellular and hemodynamic image types (Fig. 1a). For example, CHIPS is able to analyse: velocity in blood vessels based on the movement of red blood cells along a line scan; diameter of blood vessels based on either line scans across the vessel or full frame images of the vessel cross section;Footnote5 and activity in cells using a wide range of indicators.
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