Scaffold map - Integrated mapping of rat stomach data
Axon innervation, vasculature and cell density data from different experiments are mapped onto a common coordinate framework provided by the generic rat stomach scaffold.
Dataset Overview
Study Purpose: The goal of this work is to map axon innervation, vasculature and gastrin distribution data to an annotated generic rat stomach scaffold.
Data Collection: The generic rat stomach scaffold(DOI: 10.26275/iefx-c2qi) is created based on the general description and average dimensions of rat stomachs as measured by Powley et al. The data integrated in this dataset were previously mapped to a generic rat stomach scaffold individually (DOI: 10.26275/3e5x-5lp9, 10.26275/uxns-qhbq and 10.26275/litx-swak).
Primary Conclusion: None stated
Curator's Notes
Experimental Design: Not applicable.
Completeness: Complete.
Subjects & Samples: Axon innervation data derived from the segmentation of flat-mount imaging of 1 male Sprague Dawley rat stomach (DOI: 10.26275/rmcz-jfoq) is used for this mapping. The mapped vasculature data is derived from microCT imaging of 1 male Sprague Dawley rat stomachs (DOI: 10.26275/zxe9-o3ss). The mapped gastrin distribution data is derived from the antrum and corpus regions of stomachs from juvenile male Sprague-Dawley rats (n=14) (DOI: 10.26275/o9qr-l4x9).
Primary vs derivative data: The primary folder contains the mapping tool provenance data file needed to produce the scaffold map. The mapping tool will be accessible from the release download page on the SPARC Portal. The primary folder also contains the MAP-Client workflow and settings files to reproduce the files. The derivative folder contains JSON files that are used to generate a visualization of the scaffold map on the web portal.
Code Availability: Scaffold Mapping Tools
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Derived from
Fakhry, J., Stebbing, M., Hunne, B., Bayguinov, Y., Ward, S. M., Sasse, K. C., Callaghan, B., McQuade, R. M., & Furness, J. (2020). Mapping of human gastric enteroendocrine cells (Version 1) [Data set]. SPARC Portal. https://doi.org/10.26275/PPGJ-QQPF
Lin, M., Christie, R., & Hunter, P. (2022). Generic rat stomach scaffold (Version 5) [Data set]. SPARC Portal. https://doi.org/10.26275/IEFX-C2QI
Lin, M., Sorby, H., & Hunter, P. (2023). Scaffold map - Quantification of rat gastric enteroendocrine cells (Version 3) [Data set]. SPARC Portal. https://doi.org/10.26275/LITX-SWAK
Ma, J., Nguyen, D., Madas, J., Kwiat, A. M., Toledo, Z., Bizanti, A. (G., Kogut, N., Mistareehi, A., Bendowski, K., Zhang, Y., Chen, J., Li, D.-P., Powley, T. L., Furness, J., & Cheng, Z. (2023). Anterograde tracing of spinal afferent innervation in flat-mounts of the rat stomach (Version 1) [Data set]. SPARC Portal. https://doi.org/10.26275/RMCZ-JFOQ
Powley, T. L., Jaffey, D., Chesney, L., McAdams, J., & Rajwa, B. (2021). MicroCT imaging of rat stomach vasculature with Microfil MV-122 (Version 1) [Data set]. SPARC Portal. https://doi.org/10.26275/ZXE9-O3SS
Lin, M., Christie, R., & Hunter, P. (2024). Scaffold map - MicroCT imaging of rat stomach vasculature with Microfil MV-122 (Version 1) [Data set]. SPARC Portal. https://doi.org/10.26275/3E5X-5LP9
Lin, M., Christie, R., & Hunter, P. (2024). Scaffold map - Anterograde tracing of spinal afferent innervation in flat-mounts of the rat stomach (Version 1) [Data set]. SPARC Portal. https://doi.org/10.26275/UXNS-QHBQ
Is Supplemented by
Scaffold Mapping Protocol - Version 1.1.1 v3. (2022). https://doi.org/10.17504/protocols.io.n2bvj6o35lk5/v3
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