Abstract
High-resolution whole-brain microscopy provides a means for post hoc determination of the location of implanted devices and labelled cell populations that are necessary to interpret in vivo experiments designed to understand brain function. Here we have developed two plugins (brainreg and brainreg-segment) for the Python-based image viewer napari, to accurately map any object in a common coordinate space. We analysed the position of dye-labelled electrode tracks and two-photon imaged cell populations expressing fluorescent proteins. The precise location of probes and cells were physiologically interrogated and revealed accurate segmentation with near-cellular resolution.
Highlights
High-resolution whole-brain microscopy provides a means for post hoc determination of the location of implanted devices and labelled cell populations that are necessary to interpret in vivo experiments designed to understand brain function
Using napari allows other plugins to be used in combination with ours, such as those for reading of most microscopy image file formats
A second important application of the brainreg/brainreg-segment pipeline is the segmentation of brain regions according to pathological irregularities, lesions or injections. We demonstrated this feature by asking 3 experts to manually segment a brain region where neurons expressed the green fluorescent protein (GFP) using the brainreg-segment “Region segmentation” function (Fig. 2a)
Summary
High-resolution whole-brain microscopy provides a means for post hoc determination of the location of implanted devices and labelled cell populations that are necessary to interpret in vivo experiments designed to understand brain function. We have developed two plugins (brainreg and brainregsegment) for the Python-based image viewer napari, to accurately map any object in a common coordinate space. To correctly interpret the resultant data, it is critical to map the location of the implanted devices or injections, and to pool results from multiple animals in a common anatomical coordinate system. Once registered there exist no open-source, user-friendly tools for the segmentation and analysis of any type of structure in these images. We have developed brainreg and brainreg-segment, two user-friendly tools that may be used to register and segment whole-brain microscopy datasets within minutes
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