#MOUSE WARP REGISTRY SOFTWARE#
For instance, ITK-SNAP ( Yushkevich et al., 2006) is a popular biomedical software used for automatic image segmentation and delineation of regions of interest in human brain imaging data. Whole-brain volume analyses have the advantage of readily conveying the 3D spatial relationships between neuronal pathways and neighboring structures. When combined with the appropriate reference atlases (e.g., Franklin and Paxinos, 2008 Wang et al., 2020 Claudi et al., 2020), these tool kits give users the ability to reconstruct electrode tracks, viral expression, anatomical projections ( Oh et al., 2014 Zingg et al., 2014 Winnubst et al., 2019), cell types ( Fürth et al., 2018), or to detect cells ( Tyson et al., 2021), gene expression patterns, or functional nodes ( Lein et al., 2007 Ortiz et al., 2020) in the brain.ĭifferent types of tool kits have been developed for different brain preparations, including volumetric whole-brain data or sliced tissue sections, with each approach bringing its own strengths and limitations. Several software tools have been developed in recent years which use computer vision technology to accelerate and systematize the mapping of experimental results in various model species (e.g., Shamash et al., 2018 Song et al., 2020 Claudi et al., 2021 Andy, 2022).
While these and other approaches are critical for grounding experiments anatomically, doing them has become increasingly challenging with the emergence of large-scale recordings spanning multiple brain regions. Traditionally, post hoc anatomical record-keeping has relied on histological approaches where users delineate anatomical features in tissue sections, then register them manually with a reference atlas. Understanding the structure, function, or physiology of neural circuits requires the ability to consistently target brain regions prior to experiments and, afterward, to maintain an accessible, objective record of the areas studied ( Simmons and Swanson, 2009). HERBS is a multi-platform open-source Python package that is available on PyPI and GitHub, and is compatible with Windows, macOS, and Linux operating systems. Furthermore, HERBS allows users to reconstruct a 3D brain mesh with tissue from individual animals. HERBS allows users to scroll through the digital brain atlases and provides custom-angle slice cuts through the volumes, and supports free-transformation of tissue sections to atlas slices. Additionally, HERBS can delineate labeling from multiple injections across tissue sections and obtain individual cell counts.Regional delineations in HERBS are based either on annotated 3D volumes from the Waxholm Space Atlas of the Sprague Dawley Rat Brain or the Allen Mouse Brain Atlas, though HERBS can work with compatible volume atlases from any species users wish to install. Neuropixels and tetrodes), viral expression, or other anatomical features, and visualize the results in 2D or 3D. After experiments, users can register recording electrode locations (e.g. Prior to experiments, HERBS can be used to plan coordinates for implanting electrodes, targeting viral injections or tracers.
#MOUSE WARP REGISTRY REGISTRATION#
To address this we created HERBS (Histological E-data Registration in rodent Brain Spaces), a comprehensive new tool for rodent users that offers a broad range of functionalities through a user-friendly graphical user interface. This has prompted the need for digital tool kits to aid in curating anatomical data, however, existing tools either provide limited functionalities or require users to be proficient in coding to use them.
Recording technologies for rodents have seen huge advances in the last decade, allowing users to sample thousands of neurons simultaneously from multiple brain regions.
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