Synthetic-to-Real Transfer Learning for Chromatin-Sensitive PWS Microscopy

TL;DR

This paper introduces CFU Net, a hierarchical deep learning model trained on synthetic data for accurate, label-free segmentation of chromatin in microscopy images, enabling scalable early cancer detection with high accuracy and efficiency.

Contribution

The paper presents a novel synthetic data training pipeline and a specialized neural network architecture for chromatin segmentation, overcoming data annotation challenges in microscopy.

Findings

Achieved near-perfect segmentation performance on synthetic data (Dice 0.9879).

Enabled rapid, high-throughput analysis with 74.9% model compression and 0.15s inference time.

Successfully distinguished normal from pre-cancerous tissue with up to 94% accuracy.

Abstract

Chromatin sensitive partial wave spectroscopic (csPWS) microscopy enables label free detection of nanoscale chromatin packing alterations that occur before visible cellular transformation. However, manual nuclear segmentation limits population scale analysis needed for biomarker discovery in early cancer detection. The lack of annotated csPWS imaging data prevents direct use of standard deep learning methods. We present CFU Net, a hierarchical segmentation architecture trained with a three stage curriculum on synthetic multimodal data. CFU Net achieves near perfect performance on held out synthetic test data that represent diverse spectroscopic imaging conditions without manual annotations (Dice 0.9879, IoU 0.9895). Our approach uses physics based rendering that incorporates empirically supported chromatin packing statistics, Mie scattering models, and modality specific noise, combined with a curriculum that progresses from adversarial RGB pretraining to spectroscopic fine tuning and histology validation. CFU Net integrates five architectural elements (ConvNeXt backbone, Feature Pyramid Network, UNet plus plus dense connections, dual attention, and deep supervision) that together improve Dice over a baseline UNet by 8.3 percent. We demonstrate deployment ready INT8 quantization with 74.9 percent compression and 0.15 second inference, giving a 240 times throughput gain over manual analysis. Applied to more than ten thousand automatically segmented nuclei from synthetic test data, the pipeline extracts chromatin biomarkers that distinguish normal from pre cancerous tissue with large effect sizes (Cohens d between 1.31 and 2.98), reaching 94 percent classification accuracy. This work provides a general framework for synthetic to real transfer learning in specialized microscopy and open resources for community validation on clinical specimens.