The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyperparameters in different experimental settings. Here, we present a multi-modality cell segmentation benchmark, comprising over 1500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods, but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging.

Physics-driven universal twin-image removal network for digital in-line holographic microscopy

Digital in-line holographic microscopy (DIHM) enables efficient and cost-effective computational quantitative phase imaging with a large field of view, making it valuable for studying cell motility, migration, and bio-microfluidics. However, the quality of DIHM reconstructions is compromised by twin-image noise, posing a significant challenge. Conventional methods for mitigating this noise involve complex hardware setups or time-consuming algorithms with often limited effectiveness. In this work, we propose UTIRnet, a deep learning solution for fast, robust, and universally applicable twin-image suppression, trained exclusively on numerically generated datasets. The availability of open-source UTIRnet codes facilitates its implementation in various DIHM systems without the need for extensive experimental training data. Notably, our network ensures the consistency of reconstruction results with input holograms, imparting a physics-based foundation and enhancing reliability compared to conventional deep learning approaches. Experimental verification was conducted among others on live neural glial cell culture migration sensing, which is crucial for neurodegenerative disease research.

Micro Fourier Transform Profilometry ($μ$FTP): 3D shape measurement at 10,000 frames per second

Recent advances in imaging sensors and digital light projection technology have facilitated a rapid progress in 3D optical sensing, enabling 3D surfaces of complex-shaped objects to be captured with improved resolution and accuracy. However, due to the large number of projection patterns required for phase recovery and disambiguation, the maximum fame rates of current 3D shape measurement techniques are still limited to the range of hundreds of frames per second (fps). Here, we demonstrate a new 3D dynamic imaging technique, Micro Fourier Transform Profilometry ($\mu$FTP), which can capture 3D surfaces of transient events at up to 10,000 fps based on our newly developed high-speed fringe projection system. Compared with existing techniques, $\mu$FTP has the prominent advantage of recovering an accurate, unambiguous, and dense 3D point cloud with only two projected patterns. Furthermore, the phase information is encoded within a single high-frequency fringe image, thereby allowing motion-artifact-free reconstruction of transient events with temporal resolution of 50 microseconds. To show $\mu$FTP's broad utility, we use it to reconstruct 3D videos of 4 transient scenes: vibrating cantilevers, rotating fan blades, bullet fired from a toy gun, and balloon's explosion triggered by a flying dart, which were previously difficult or even unable to be captured with conventional approaches.