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Bioinformatics Live Coding Session - alignment of spatial transcriptomics data using STalign

I record myself coding to perform an exploratory analysis where I structurally align a single-cell resolution spatial transcriptomics dataset profiled by the Xenium technology with a multi-cellular pixel resolution spatial transcriptomics profiled by the Visium technology from 10X Genomics of two serial breast cancer tumor tissue sections using our lab's bioinformatics Python tool STalign. I hope this will help give students a sense for how I would go about performing spatial structural alignment using STalign, the kinds of challenges I face and how I try to address them, and the types of 'sanity checks' I like to perform along the way (mainly lots of visualizations). Code along or download the complete notebook: https://github.com/JEFworks/coding_vi... I'm trying out some different styles for these living coding videos. In this case, I've sped myself up around 200% to 400% and did a voiceover narration instead of live narrating as I did in previous videos in order to make the video shorter. So please be aware, I don't actually code that fast! Additional resources: - STalign source code on Github: https://github.com/JEFworks-Lab/STalign - STalign's documentation: https://jef.works/STalign/ - Open-access paper describing STalign: https://www.nature.com/articles/s4146... - Video transcript available on lab website: https://jef.works/blog/2023/12/27/ali... Some potentially helpful moments: - Downloading these publicly available spatial transcriptomics datasets:    • Bioinformatics Live Coding Session - ...   - Reading and processing spatial transcriptomics data for alignment with STalign:    • Bioinformatics Live Coding Session - ...   - Using STalign's point annotator tool to place manual landmarks to guide an initial affine alignment:    • Bioinformatics Live Coding Session - ...   - Performing a landmark-based affine alignment with STalign:    • Bioinformatics Live Coding Session - ...   - Performing a diffeomorphic alignment with STalign:    • Bioinformatics Live Coding Session - ...   - Checking results:    • Bioinformatics Live Coding Session - ...