microscopy image analysts

Abstract: In retinal vessel segmentation, plain Vision Transformers (ViTs) are commonly expected to perform worse than convolutional neural networks (CNNs) on thin vessels, for reasons such as their coarse patch tokenization, their weak locality bias and their need for large training sets. Although this expectation is widely shared in the literature, how plain ViTs actually compare with CNNs on thin vessels has not been systematically quantified. We address this question by comparing a model with a plain ViT encoder (MedSAM), a hybrid Transformer (LiteMedSAM) and three CNNs of different sizes on three retinal datasets (DRIVE, HRF, FIVES) and, as a second-domain check, a microscopy dataset (VessMap). We measured the centerline recall and precision of thin vessels and compared the models while also considering their computational cost and how many epochs they needed to train. We found that the pre-trained MedSAM had a centerline recall of thin vessels that was not significantly different from that of the best CNN on all four datasets (-0.6 to +2.5 percentage points). A compact plain ViT obtained through architecture search but trained from scratch did not retain this performance. For pre-trained plain ViTs, our results do not support the expectation that they miss thin vessels, although similar thin-vessel performance can be obtained with much smaller models.

Abstract: Diffusion-based denoising commonly uses Gaussian perturbations, whereas sensor noise follows diverse signal-dependent statistical laws. In this paper, we propose $p$-Bridge, a unified measurement-indexed diffusion framework for Tweedie noise. The noise exponent $p$ describes the variance--intensity relation, while accumulated measurement $ν$ controls the noise level. Together, they define a noise plane that includes Gaussian, Poisson, and Gamma models. The stochastic bridge connects measurement distributions through independent increments, giving denoising a physical interpretation as progressive measurement accumulation. Both the starting and stopping indices can be specified, allowing restoration from an observed measurement level to a prescribed higher level. Measurement superposition yields a shared reverse-mean update, paired with a deviance-based objective for learning the required conditional mean. A latent compound Poisson--Gamma construction enables sampling at intermediate exponents. A single exponent-conditioned network adapts to different Tweedie noise models without separate training for each exponent. Experiments show that exponent conditioning improves cross-exponent robustness over fixed-exponent models. Using estimated exponents, the shared network achieves robustness comparable to an oracle-selected set of five specialist models. Experiments on synthetic images, FMD fluorescence microscopy, and multi-sensor SAR images further demonstrate its effectiveness across different signal-dependent noise regimes.

Abstract: 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 ($\text{SNR} = σ_s^2/σ_n^2$ < 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 ($-20\text{ dB}$). 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.