URL: https://github.com/mjin1812/SMART
Proper Citation: Semi-Manual Alignment to Reference Templates (RRID:SCR_019265)
Description: Software tool that extends WholeBrain framework in R for segmenting and registering experimental images to Allen Mouse Common Coordinate Framework (CCF). Streamlines processing of large volumetric LSFM datasets and solves issues with non-uniform morphing across anterior-posterior axis with interactive “choice game.” Accounts for duplicate cell counts in adjacent z images and presents new ways to easily parse apart and interactively visualize final mapped datasets.
Abbreviations: SMART
Resource Type: image analysis software, software application, segmentation software, software resource, data processing software
Defining Citation: DOI:10.1101/727529
Keywords: Segmenting experimental images, registering experimental images, Allen Mouse Common Coordinate Framework, data processing, experimental images
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