MERFISH Barcode Decoding

Imaging-based spatial transcriptomics methods like MERFISH identify individual mRNA molecules in place, inside intact tissue, without sequencing anything. Each gene is assigned a binary barcode read out across sequential rounds of hybridization and imaging: a molecule blinks on in round i exactly when bit i of its gene's codeword is 1. This simulator renders a 3D field of single molecules cycling through those rounds, flashing their observed bit pattern, then decodes each one against a real error-correcting codebook (fixed Hamming weight, minimum pairwise distance 4) built live from the barcode length you choose. A per-round error-rate slider injects realistic dropout and false-positive noise, and a toggle lets you compare naive exact-match decoding against the nearest-codeword error correction real MERFISH pipelines use — watch the accuracy, corrected-molecule count, and no-call rate respond live.