DeepSlice Source Data and Ground Truth datasets

Hi! Welcome to the DeepSlice data repository!This repository contains:Source data used to generate the graphs shown in Figures 1, 2 & 3 of Carey et al. (2023).Histological images and alignment data used to guide the development of, and assess the performance of, the DeepSlice algorithm.Code you can use to replicate the DeepSlice alignment filesSources data are organised in Excel spreadsheets, with data corresponding to each panel itemised in separate worksheets (Figure 1.xlsx, Figure 2.xlsx, Figure 3.xlsx).Histological images corresponding to Ground Truth datasets are saved in .Zip files.The following zip repositories are included:NameSource DOIGLT1a10.25493/Y147-2CEPcP210.25493/A2EG-VPRCamKII10.25493/W97C-01RCalb1http://mouse.brain-map.org/experiment/show/71717640β amyloidprovided by Yates et al. 10.3389/fninf.2019.00075Myelin10.25493/Y147-2CEPitx310.25493/DTB3-0KPThe GLT1a, PcP2, CamKII, Myelin & Pitx3 datasets are made available from eBrains via CC4.0 license. Calb1 dataset is courtesy of the Allen Institute for Brain Science. Allen Mouse Brain Atlas dataset# 71717640 Available from mouse.brain-map.org. Allen Institute for Brain Science (2011).The β amyloid dataset is courtesy of Yates et al.Alignment metadata, generated by human or DeepSlice, are provided as .xml and .csv files in corresponding Zip archives. To view human- or DeepSlice-generated alignments save image files and .xml files to the same directory and load in QuickNII (https://www.nitrc.org/projects/quicknii). The DeepSlice source code, and tools used to calculate differences in alignments, are available at https://github.com/PolarBean/DeepSliceWe hope you find this useful, either as a way of validating or replicating our work or as a means to quantify the performance of other alignment algorithms. Don't forget to cite our paper if you do!Harry Carey, Michael Pegios, Lewis Martin, Chris Saleeba, Anita J. Turner, Nicholas Everett, Maja A. Puchades, Jan G. Bjaalie & Simon McMullan (2023) DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas, Nature Communications, DOI:10.1038/s41467-023-41645-4