Disentangling coincident cell events using deep transfer learning and compressive sensing

TL;DR

This paper introduces a hybrid deep learning and compressive sensing framework to accurately disentangle overlapping single-cell signals, improving detection and characterization in non-optical cytometry methods.

Contribution

The novel hybrid FCN and CS approach effectively separates coincident cell events in sensor data, outperforming traditional algorithms and enabling detailed single-cell analysis without retraining.

Findings

Recovered up to 21% more events than state-machine algorithms.

Achieved classification accuracy beyond 97%.

Demonstrated compatibility with various waveform modalities.

Abstract

Accurate single-cell analysis is critical for diagnostics, immunomonitoring, and cell therapy, but coincident events - where multiple cells overlap in a sensing zone - can severely compromise signal fidelity. We present a hybrid framework combining a fully convolutional neural network (FCN) with compressive sensing (CS) to disentangle such overlapping events in one-dimensional sensor data. The FCN, trained on bead-derived datasets, accurately estimates coincident event counts and generalizes to immunomagnetically labeled CD4+ and CD14+ cells in whole blood without retraining. Using this count, the CS module reconstructs individual signal components with high fidelity, enabling precise recovery of single-cell features, including velocity, amplitude, and hydrodynamic diameter. Benchmarking against conventional state-machine algorithms shows superior performance - recovering up to 21% more events and improving classification accuracy beyond 97%. Explinability via class activation maps and parameterized Gaussian template fitting ensures transparency and clinical interpretability. Demonstrated with magnetic flow cytometry (MFC), the framework is compatible with other waveform-generating modalities, including impedance cytometry, nanopore, and resistive pulse sensing. This work lays the foundation for next-generation non-optical single-cell sensing platforms that are automated, generalizable, and capable of resolving overlapping events, broadening the utility of cytometry in translational medicine and precision diagnostics, e.g. cell-interaction studies.