I cant tell you how helpful that repository is, We always need more data, especially high quality alignments so that is fantastic. Thank you!
At present DeepSlice only works with coronal sections, not sagittal or axial but thats just due to the training data. We hope to build a version that can align all orientations soon. I cant really see too well in the image you posted but your section looks axial? Im keen to see how DeepSlice performs on your coronal data.
As for downsampling large sections, this is primarily so as we dont crush our bandwidth limits. DeepSlice is actually a python package and when we release it, it will work on full resolution images but I would still recommend downsampling as this is necessary to open your sections in QuickNII. @NicoKiaru is working on this functionality for his ABBA tool which should streamline the process.
Thank you again for the data, I will update you on how I go integrating this with our training set.