3D Holographic Observatory for Long-term Monitoring of Complex Behaviors in Drosophila

Digital in-line holographic microscopy for label-free identification and tracking of biological cells

Digital in-line holographic microscopy (DIHM) is a non-invasive, real-time, label-free technique that captures three-dimensional (3D) positional, orientational, and morphological information from digital holographic images of living biological cells. Unlike conventional microscopies, the DIHM technique enables precise measurements of dynamic behaviors exhibited by living cells within a 3D volume. This review outlines the fundamental principles and comprehensive digital image processing procedures employed in DIHM-based cell tracking methods. In addition, recent applications of DIHM technique for label-free identification and digital tracking of various motile biological cells, including human blood cells, spermatozoa, diseased cells, and unicellular microorganisms, are thoroughly examined. Leveraging artificial intelligence has significantly enhanced both the speed and accuracy of digital image processing for cell tracking and identification. The quantitative data on cell morphology and dynamics captured by DIHM can effectively elucidate the underlying mechanisms governing various microbial behaviors and contribute to the accumulation of diagnostic databases and the development of clinical treatments.

Effect of hologram plane position on particle tracking using digital holographic microscopy

This paper discusses the effect of hologram plane position on the tracking of particle motions in a 3D suspension using digital holography microscopy. We compare two optical configurations where the hologram plane is located either just outside the particle suspension or in the middle of the suspension. In both cases, we record two axially separated holograms using two cameras and subsequently adopt an iterative phase retrieval approach to solve the virtual image problem. We measure the settling motions of 2 µm spheres in a 2 mm thick sample containing 300 to 1500p a r t i c l e s/m m ³. We show that the optical setup where the hologram plane is located in the middle of the sample provides superior tracking results compared to the other, including higher accuracy in the measurement of particle displacement and longer particle trajectories. The accuracy of particle displacement increases by a maximum of 18%, and the trajectory length increases by a maximum of 16%. This superior outcome is due to the less overlapping of the diffraction patterns on the holograms when the separation distance between particles and the hologram plane is minimized.

Kinematic analysis and visualization of Tetraselmis microalgae 3D motility by digital holography

A study on locomotion in a 3D environment of Tetraselmis microalgae by digital holographic microscopy is reported. In particular, a fast and semiautomatic criterion is revealed for tracking and analyzing the swimming path of a microalga (i.e., Tetraselmis species) in a 3D volume. Digital holography (DH) in a microscope off-axis configuration is exploited as a useful method to enable fast autofocusing and recognition of objects in the field of view, thus coupling DH with appropriate numerical algorithms. Through the proposed method we measure, simultaneously, the tri-dimensional paths followed by the flagellate microorganism and the full set of the kinematic parameters that describe the swimming behavior of the analyzed microorganisms by means of a polynomial fitting and segmentation. Furthermore, the method is capable to furnish the accurate morphology of the microorganisms at any instant of time along its 3D trajectory. This work launches a promising trend having as the main objective the combined use of DH and motility microorganism analysis as a label-free and non-invasive environmental monitoring tool, employable also for in situ measurements. Finally, we show that the locomotion can be visualized intriguingly by different modalities to furnish marine biologists with a clear 3D representation of all the parameters of the kinematic set in order to better understand the behavior of the microorganism under investigation.

Improving axial localization of weak phase particles in digital in-line holography

One shortcoming of digital in-line holography (DIH) is the low axial position accuracy due to the elongated particle traces in the reconstruction field. Here, we propose a method that improves the axial localization of DIH when applying it to track the motion of weak phase particles in dense suspensions. The proposed method detects particle positions based on local intensities in the reconstruction field consisting of scattering and incident waves. We perform both numerical and experimental tests and demonstrate that the proposed method has a higher axial position accuracy than the previous method based on the local intensities in the reconstructed scattered field. We show that the proposed method has an axial position error below 1.5 particle diameters for holograms with a particle concentration of 4700particles/mm³. The proposed method is further validated by tracking the Brownian motion of 1µmparticles in dense suspensions.

Rodent and fly models in behavioral neuroscience: An evaluation of methodological advances, comparative research, and future perspectives

The assessment of behavioral outcomes is a central component of neuroscientific research, which has required continuous technological innovations to produce more detailed and reliable findings. In this article, we provide an in-depth review on the progress and future implications for three model organisms (mouse, rat, and Drosophila) essential to our current understanding of behavior. By compiling a comprehensive catalog of popular assays, we are able to compare the diversity of tasks and usage of these animal models in behavioral research. This compilation also allows for the evaluation of existing state-of-the-art methods and experimental applications, including optogenetics, machine learning, and high-throughput behavioral assays. We go on to discuss novel apparatuses and inter-species analyses for centrophobism, feeding behavior, aggression and mating paradigms, with the goal of providing a unique view on comparative behavioral research. The challenges and recent advances are evaluated in terms of their translational value, ethical procedures, and trustworthiness for behavioral research.

Machine learning holography for 3D particle field imaging

We propose a new learning-based approach for 3D particle field imaging using holography. Our approach uses a U-net architecture incorporating residual connections, Swish activation, hologram preprocessing, and transfer learning to cope with challenges arising in particle holograms where accurate measurement of individual particles is crucial. Assessments on both synthetic and experimental holograms demonstrate a significant improvement in particle extraction rate, localization accuracy and speed compared to prior methods over a wide range of particle concentrations, including highly dense concentrations where other methods are unsuitable. Our approach can be potentially extended to other types of computational imaging tasks with similar features.

Regularized inverse holographic volume reconstruction for 3D particle tracking

The key limitations of digital inline holography (DIH) for particle tracking applications are poor longitudinal resolution, particle concentration limits, and case-specific processing. We utilize an inverse problem method with fused lasso regularization to perform full volumetric reconstructions of particle fields. By exploiting data sparsity in the solution and utilizing GPU processing, we dramatically reduce the computational cost usually associated with inverse reconstruction approaches. We demonstrate the accuracy of the proposed method using synthetic and experimental holograms. Finally, we present two practical applications (high concentration microorganism swimming and microfiber rotation) to extend the capabilities of DIH beyond what was possible using prior methods.