Accurate phenotyping of cells in the tumor microenvironment is essential for understanding cancer biology but typically requires precise cell segmentation, limiting scalability. Here, we introduce Contrastive Learning Enabled Accurate Registration of Immune and Tumor cells (CLEAR-IT), a self-supervised framework that learns cell-level features from multiplexed images using only cell locations. CLEAR-IT encoders achieve strong linear evaluation performance, improve substantially with hyperparameter optimization, and maintain high accuracy across imaging modalities and with up to 90% fewer labels. When substituted for handcrafted features in a state-of-the-art classifier, CLEAR-IT features yield higher performance, and their combination enables comparable accuracy with less than half of the labeled data otherwise required. The learned representations also support prognostic modeling: using annotations from a single patient, CLEAR-IT-based phenotyping identifies survival-associated tissue features that generalize across two cohorts and modalities. CLEAR-IT provides a segmentation-light, label-efficient approach for scalable cell phenotyping and enhances existing workflows in digital pathology and tumor microenvironment analysis.

Super-resolution microscopy (SRM) has undeniable potential for scientific discovery, yet still presents many challenges that hinder its widespread adoption, including technical trade-offs between resolution, speed and photodamage, as well as limitations in imaging live samples and larger, more complex biological structures. Furthermore, SRM often requires specialized expertise and complex instrumentation, which can deter biologists from fully embracing the technology. In this Perspective, a follow-up to our recent Q&A article, we aim to demystify these challenges by addressing common questions and misconceptions surrounding SRM. Experts offer practical insights into how biologists can maximize the benefits of SRM while navigating issues such as photobleaching, image artifacts and the limitations of existing techniques. We also highlight recent developments in SRM that continue to push the boundaries of resolution. Our goal is to equip researchers with the crucial knowledge they need to harness the full potential of SRM.

In single-molecule microscopy, a big question is how precisely we can estimate the location of a single molecule. Our research shows that by using iterative localisation microscopy and factoring in the prior information, we can boost precision and reduce the number of photons needed. Leveraging the Van Trees inequality aids in determining the optimal precision achievable. Our approach holds promise for wider application in discerning the optimal precision across diverse imaging scenarios, encompassing various illumination strategies, point spread functions and overarching control methodologies.

Super-resolution microscopy (SRM) is gaining popularity in biosciences; however, claims about optical resolution are contested and often misleading. In this Viewpoint, experts share their views on resolution and common trade-offs, such as labelling and post-processing, aiming to clarify them for biologists and facilitate deeper understanding and best use of SRM.