# FPicker: Topology-Guided Evolution for Filament Tracing in Low-SNR Microscopy

arXiv: https://arxiv.org/abs/2609.08305 · HTML: https://mlsanity.com/paper/2609.08305/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 21 of its 47 references that are in the map.
- First posted on arXiv 8 Sep 2026.

## Builds on (most cited first, 21 of 21)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [SegFormer: Simple and Efficient Design for Semantic Segmentation with Transformers](https://mlsanity.com/paper/2105.15203/) (2021)
- [SAM 2: Segment Anything in Images and Videos](https://mlsanity.com/paper/2408.00714/) (2024)
- [Objects as Points](https://mlsanity.com/paper/1904.07850/) (2019)
- [DETRs Beat YOLOs on Real-time Object Detection](https://mlsanity.com/paper/2304.08069/) (2023)
- [YOLOv10: Real-Time End-to-End Object Detection](https://mlsanity.com/paper/2405.14458/) (2024)
- [Deep Layer Aggregation](https://mlsanity.com/paper/1707.06484/) (2017)
- [U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation](https://mlsanity.com/paper/2401.04722/) (2024)
- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [Deep Snake for Real-Time Instance Segmentation](https://mlsanity.com/paper/2001.01629/) (2020)
- [RoadTracer: Automatic Extraction of Road Networks from Aerial Images](https://mlsanity.com/paper/1802.03680/) (2018)
- [Fast Interactive Object Annotation with Curve-GCN](https://mlsanity.com/paper/1903.06874/) (2019)
- [DeepVesselNet: Vessel Segmentation, Centerline Prediction, and Bifurcation Detection in 3-D Angiographic Volumes](https://mlsanity.com/paper/1803.09340/) (2018)
- [DeepLSD: Line Segment Detection and Refinement with Deep Image Gradients](https://mlsanity.com/paper/2212.07766/) (2022)
- [Learning deep structured active contours end-to-end](https://mlsanity.com/paper/1803.06329/) (2018)
- [Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs](https://mlsanity.com/paper/1803.08207/) (2018)
- [Reformulating Level Sets as Deep Recurrent Neural Network Approach to Semantic Segmentation](https://mlsanity.com/paper/1704.03593/) (2017)
- [Deep Reinforcement Learning for Small Bowel Path Tracking using Different Types of Annotations](https://mlsanity.com/paper/2206.14847/) (2022)

## Abstract (arXiv)

Automating filament tracing in Cryo-Electron Microscopy (Cryo-EM) is essential for 3D helical reconstruction but challenged by intersecting topologies and extremely low Signal-to-Noise Ratios (SNR = σs2/σn2 < 0.1 or -10 dB). Existing paradigms fail: pixel-wise segmenters suffer from severe topological fracturing, box-based detectors face ghost center drift, sequential trackers derail due to error accumulation, and traditional active contours collapse under artificial closed-curve constraints. To resolve these bottlenecks, we present FPicker, the first topology-guided framework reconciling these incompatibilities. It unifies perception via a center-endpoint representation and an open-curve evolution module to explicitly model non-cyclic connectivity. On simulated benchmarks, FPicker outperforms top baselines by over 40% relative gain in mean spatio-angular precision (mSAP) and reduces topological gap rates by over 60% under extreme noise (-20 dB). By learning intrinsic physical geometry rather than local texture, FPicker demonstrates strong potential as a resilient geometric backbone. Its zero-shot performance on the real-world EMPIAR dataset exhibits robust topological resistance, achieving a state-of-the-art 82.9% mSAP upon fine-tuning. Our results also suggest modeling physical priors is a highly robust path toward bridging the sim-to-real gap in signal-starved scientific imaging. The code is publicly available at: https://github.com/tomzhaosky/FPicker.