Make Shapes and Signals Meet: A Gentle Guide to BCPD and DET

Make Shapes and Signals Meet is an illustrated, beginner-friendly guide to BCPD and DET. BCPD aligns shapes using point locations, while DET also uses signal information—such as image intensities, audio amplitudes, or gene-expression features—to guide registration. The guide introduces the algorithms and related methods, including BCPD++, GBCPD, and DLD. It provides practical instructions for installation, running Python demonstrations, visualizing and saving results, choosing parameters and kernels, using hierarchical registration, and reducing computation time and memory. It also explains output files and demonstrates how to assess registration quality. Examples cover point clouds, anatomical meshes, images, audio signals, and spatial transcriptomics, including MERFISH and MOSTA. A two-page Quick Reference summarizes common commands, parameters, and outputs. This edition is Manual v0.99 and describes software v0.99. The software and links to demonstration data are available at https://github.com/ohirose/bcpd. Original text and illustrations are licensed under CC BY 4.0, except where otherwise indicated. Third-party material retains its original rights and applicable terms; see the captions and credits.