PhySeqNet: physics-informed fluorescent foci detection for BARseq spatial transcriptomics

Abstract

BARseq enables spatially resolved gene-expression profiling across intact tissue, but its sensitivity depends on accurate detection and decoding of dense fluorescent rolonies. Existing spot-calling approaches can be conservative where signals overlap, while supervised deep learning is limited by the lack of reliable manual ground truth in real tissue images. Here we present PhySeqNet, a physics-informed deep learning framework for annotation-free fluorescent foci detection in BARseq. PhySeqNet trains U-Net detectors entirely on semi-synthetic images generated from an instrument-matched optical model combined with real sample-free experimental noise, and is integrated into pyBARseq, a modular Python pipeline for BARseq analysis. PhySeqNet achieved high detection performance on held-out simulated data across wavelength bands. On real tissue images, where ground truth is unavailable, we evaluated detections by forward-model reconstruction: PhySeqNet with conservative barcode-aware non-maxima suppression (NMSB) achieved higher reconstruction fidelity (NCC and MS-SSIM) than the BarDensr single-shot estimator, tuned classical spot detectors, and a pretrained deep-learning detector. In the analyzed brain section, PhySeqNet with NMSB yielded a median of 51 counts per cell versus 47 for BarDensr, with a similar number of genes detected per cell. The recovered transcripts produced spatial expression patterns qualitatively consistent with Allen MERFISH reference data and preserved cell-type composition after scANVI label transfer. These results show that physics-informed simulation can train practical, annotation-free detectors that improve BARseq sensitivity without disrupting downstream biological interpretation.