OME-Zarr: a cloud-optimized bioimaging file format with international community support.

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself-OME-Zarr-along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain-the file format that underlies so many personal, institutional, and global data management and analysis tasks.

Data-driven microscopy allows for automated context-specific acquisition of high-fidelity image data.

Light microscopy is a powerful single-cell technique that allows for quantitative spatial information at subcellular resolution. However, unlike flow cytometry and single-cell sequencing techniques, microscopy has issues achieving high-quality population-wide sample characterization while maintaining high resolution. Here, we present a general framework, data-driven microscopy (DDM) that uses real-time population-wide object characterization to enable data-driven high-fidelity imaging of relevant phenotypes based on the population context. DDM combines data-independent and data-dependent steps to synergistically enhance data acquired using different imaging modalities. As a proof of concept, we develop and apply DDM with plugins for improved high-content screening and live adaptive microscopy for cell migration and infection studies that capture events of interest, rare or common, with high precision and resolution. We propose that DDM can reduce human bias, increase reproducibility, and place single-cell characteristics in the context of the sample population when interpreting microscopy data, leading to an increase in overall data fidelity.

OME-Zarr: a cloud-optimized bioimaging file format with international community support.

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself -- OME-Zarr -- along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain -- the file format that underlies so many personal, institutional, and global data management and analysis tasks.

An open-source microscopy framework for simultaneous control of image acquisition, reconstruction, and analysis.

We present a computational framework to simultaneously perform image acquisition, reconstruction, and analysis in the context of open-source microscopy automation. The setup features multiple computer units intersecting software with hardware devices and achieves automation using python scripts. In practice, script files are executed in the acquisition computer and can perform any experiment by modifying the state of the hardware devices and accessing experimental data. The presented framework achieves concurrency by using multiple instances of ImSwitch and napari working simultaneously. ImSwitch is a flexible and modular open-source software package for microscope control, and napari is a multidimensional image viewer for scientific image analysis. The presented framework implements a system based on file watching, where multiple units monitor a filesystem that acts as the synchronization primitive. The proposed solution is valid for any microscope setup, supporting various biological applications. The only necessary element is a shared filesystem, common in any standard laboratory, even in resource-constrained settings. The file watcher functionality in Python can be easily integrated into other python-based software. We demonstrate the proposed solution by performing tiling experiments using the molecular nanoscale live imaging with sectioning ability (MoNaLISA) microscope, a high-throughput super-resolution microscope based on reversible saturable optical fluorescence transitions (RESOLFT).

Deep learning-enhanced light-field imaging with continuous validation.

Visualizing dynamic processes over large, three-dimensional fields of view at high speed is essential for many applications in the life sciences. Light-field microscopy (LFM) has emerged as a tool for fast volumetric image acquisition, but its effective throughput and widespread use in biology has been hampered by a computationally demanding and artifact-prone image reconstruction process. Here, we present a framework for artificial intelligence-enhanced microscopy, integrating a hybrid light-field light-sheet microscope and deep learning-based volume reconstruction. In our approach, concomitantly acquired, high-resolution two-dimensional light-sheet images continuously serve as training data and validation for the convolutional neural network reconstructing the raw LFM data during extended volumetric time-lapse imaging experiments. Our network delivers high-quality three-dimensional reconstructions at video-rate throughput, which can be further refined based on the high-resolution light-sheet images. We demonstrate the capabilities of our approach by imaging medaka heart dynamics and zebrafish neural activity with volumetric imaging rates up to 100 Hz.

BigDataProcessor2: a free and open-source Fiji plugin for inspection and processing of TB sized image data.

SUMMARY: Modern bioimaging and related areas such as sensor technology have undergone tremendous development over the last few years. As a result, contemporary imaging techniques, particularly electron microscopy (EM) and light sheet microscopy, can frequently generate datasets attaining sizes of several terabytes (TB). As a consequence, even seemingly simple data operations such as cropping, chromatic- and drift-corrections and even visualisation, poses challenges when applied to thousands of time points or tiles. To address this we developed BigDataProcessor2-a Fiji plugin facilitating processing workflows for TB sized image datasets. AVAILABILITY AND IMPLEMENTATION: BigDataProcessor2 is available as a Fiji plugin via the BigDataProcessor update site. The application is implemented in Java and the code is publicly available on GitHub (https://github.com/bigdataprocessor/bigdataprocessor2). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cell and tissue manipulation with ultrashort infrared laser pulses in light-sheet microscopy.

Three-dimensional live imaging has become an indispensable technique in the fields of cell, developmental and neural biology. Precise spatio-temporal manipulation of biological entities is often required for a deeper functional understanding of the underlying biological process. Here we present a home-built integrated framework and optical design that combines three-dimensional light-sheet imaging over time with precise spatio-temporal optical manipulations induced by short infrared laser pulses. We demonstrate their potential for sub-cellular ablation of neurons and nuclei, tissue cauterization and optogenetics by using the Drosophila melanogaster and zebrafish model systems.

Instantaneous isotropic volumetric imaging of fast biological processes.

To capture highly dynamic biological processes at cellular resolution is a recurring challenge in biology. Here we show that combining selective-volume illumination with simultaneous acquisition of orthogonal light fields yields three-dimensional images with high, isotropic spatial resolution and a significant reduction of reconstruction artefacts, thereby overcoming current limitations of light-field microscopy implementations. We demonstrate medaka heart and blood flow imaging at single-cell resolution and free of motion artefacts at volume rates of up to 200 Hz.

Clearance by Microglia Depends on Packaging of Phagosomes into a Unique Cellular Compartment.

Phagocytic immune cells such as microglia can engulf and process pathogens and dying cells with high efficiency while still maintaining their dynamic behavior and morphology. Effective intracellular processing of ingested cells is likely to be crucial for microglial function, but the underlying cellular mechanisms are poorly understood. Using both living fish embryos and mammalian macrophages, we show that processing depends on the shrinkage and packaging of phagosomes into a unique cellular compartment, the gastrosome, with distinct molecular and ultra-structural characteristics. Loss of the transporter Slc37a2 blocks phagosomal shrinkage, resulting in the expansion of the gastrosome and the dramatic bloating of the cell. This, in turn, affects the ability of microglia to phagocytose and migrate toward brain injuries. Thus, this work identifies a conserved crucial step in the phagocytic pathway of immune cells and provides a potential entry point for manipulating their behavior in development and disease.

Spinal cord injury in zebrafish induced by near-infrared femtosecond laser pulses.

BACKGROUND: The spinal cord is composed of a large number of cells that interact to allow the organism to function. To perform detail studies of cellular processes involved in spinal cord injury (SCI), one must use repeatable and specific methods to target and injure restricted areas of the spinal cord. NEW METHOD: We propose a robust method to induce SCI in zebrafish by laser light. With a 2-photon microscope equipped with a femtosecond near-infrared pump laser, we explored the effects of laser beam exposure time, area, and intensity to induce precise and repeatable SCI with minimized collateral damage to neighboring cells. RESULTS: Through behavioral studies in zebrafish larvae, we assessed the functional outcome of intensive laser light directed at the spinal cord. Our experiments revealed that a laser pulse with wavelength 800 nm, duration 2.6 ms, and light intensity 390 mW was sufficient to induce controlled cell death in a single cell or a spinal cord segment. Collateral damage was observed if cells were exposed to laser pulses exceeding 470 mW. With these settings, we could induce precise and repeatable SCI in zebrafish larvae, resulting in loss of motor and sensory function. COMPARISON WITH EXISTING METHOD(S): Our method offers a simple and more controlled setting to induce SCI in zebrafish. We describe how the near-infrared femtosecond laser should be adjusted for achieving optimal results with minimal collateral damage. CONCLUSIONS: We present a precise and robust method for inducing SCI in zebrafish with single-cell resolution using femtosecond near-infrared laser pulses.

Breaking the diffraction limit of light-sheet fluorescence microscopy by RESOLFT.

We present a plane-scanning RESOLFT [reversible saturable/switchable optical (fluorescence) transitions] light-sheet (LS) nanoscope, which fundamentally overcomes the diffraction barrier in the axial direction via confinement of the fluorescent molecular state to a sheet of subdiffraction thickness around the focal plane. To this end, reversibly switchable fluorophores located right above and below the focal plane are transferred to a nonfluorescent state at each scanning step. LS-RESOLFT nanoscopy offers wide-field 3D imaging of living biological specimens with low light dose and axial resolution far beyond the diffraction barrier. We demonstrate optical sections that are thinner by 5-12-fold compared with their conventional diffraction-limited LS analogs.

Inverted light-sheet microscope for imaging mouse pre-implantation development.

Despite its importance for understanding human infertility and congenital diseases, early mammalian development has remained inaccessible to in toto imaging. We developed an inverted light-sheet microscope that enabled us to image mouse embryos from zygote to blastocyst, computationally track all cells and reconstruct a complete lineage tree of mouse pre-implantation development. We used this unique data set to show that the first cell fate specification occurs at the 16-cell stage.

Confocal multiview light-sheet microscopy.

Selective-plane illumination microscopy has proven to be a powerful imaging technique due to its unsurpassed acquisition speed and gentle optical sectioning. However, even in the case of multiview imaging techniques that illuminate and image the sample from multiple directions, light scattering inside tissues often severely impairs image contrast. Here we combine multiview light-sheet imaging with electronic confocal slit detection implemented on modern camera sensors. In addition to improved imaging quality, the electronic confocal slit detection doubles the acquisition speed in multiview setups with two opposing illumination directions allowing simultaneous dual-sided illumination. Confocal multiview light-sheet microscopy eliminates the need for specimen-specific data fusion algorithms, streamlines image post-processing, easing data handling and storage.

Near infrared optical projection tomography for assessments of ß-cell mass distribution in diabetes research.

By adapting OPT to include the capability of imaging in the near infrared (NIR) spectrum, we here illustrate the possibility to image larger bodies of pancreatic tissue, such as the rat pancreas, and to increase the number of channels (cell types) that may be studied in a single specimen. We further describe the implementation of a number of computational tools that provide: 1/ accurate positioning of a specimen's (in our case the pancreas) centre of mass (COM) at the axis of rotation (AR); 2/ improved algorithms for post-alignment tuning which prevents geometric distortions during the tomographic reconstruction and 3/ a protocol for intensity equalization to increase signal to noise ratios in OPT-based BCM determinations. In addition, we describe a sample holder that minimizes the risk for unintentional movements of the specimen during image acquisition. Together, these protocols enable assessments of BCM distribution and other features, to be performed throughout the volume of intact pancreata or other organs (e.g. in studies of islet transplantation), with a resolution down to the level of individual islets of Langerhans.

Aggregation and fibril morphology of the Arctic mutation of Alzheimer's Aß peptide by CD, TEM, STEM and in situ AFM.

Morphology of aggregation intermediates, polymorphism of amyloid fibrils and aggregation kinetics of the "Arctic" mutant of the Alzheimer's amyloid ß-peptide, Aß((1-40))(E22G), in a physiologically relevant Tris buffer (pH 7.4) were thoroughly explored in comparison with the human wild type Alzheimer's amyloid peptide, wt-Aß((1-40)), using both in situ atomic force and electron microscopy, circular dichroism and thioflavin T fluorescence assays. For arc-Aß((1-40)) at the end of the 'lag'-period of fibrillization an abrupt appearance of ≈ 3 nm size 'spherical aggregates' with a homogeneous morphology, was identified. Then, the aggregation proceeds with a rapid growth of amyloid fibrils with a variety of morphologies, while the spherical aggregates eventually disappeared during in situ measurements. Arc-Aß((1-40)) was also shown to form fibrils at much lower concentrations than wt-Aß((1-40)): ≤ 2.5 µM and 12.5 µM, respectively. Moreover, at the same concentration, 50 µM, the aggregation process proceeds more rapidly for arc-Aß((1-40)): the first amyloid fibrils were observed after c.a. 72 h from the onset of incubation as compared to approximately 7 days for wt-Aß((1-40)). Amyloid fibrils of arc-Aß((1-40)) exhibit a large variety of polymorphs, at least five, both coiled and non-coiled distinct fibril structures were recognized by AFM, while at least four types of arc-Aß((1-40)) fibrils were identified by TEM and STEM and their mass-per-length statistics were collected suggesting supramolecular structures with two, four and six ß-sheet laminae. Our results suggest a pathway of fibrillogenesis for full-length Alzheimer's peptides with small and structurally ordered transient spherical aggregates as on-pathway immediate precursors of amyloid fibrils.

On the quantitative molecular analysis of electronic energy transfer within donor-acceptor pairs.

An extended Förster theory (EFT) on electronic energy transfer is presented for the quantitative analysis of time-resolved fluorescence lifetime and depolarisation experiments. The EFT, which was derived from the stochastic Liouville equation, yields microscopic information concerning the reorientation correlation times, the order parameters, as well as inter chromophoric distances. Weakly interacting donor and acceptor groups, which reorient and interact in a pair wise fashion, are considered, under isotropic and anisotropic conditions. For the analysis of experiments it is shown that not only do we need to consider the orientational distributions of the transition dipoles, but the internal reorienting molecular dynamics within the pair which is of even greater importance. The latter determines the shape as well as the rate of the observed donor fluorescence and depolarisation decays, which are most often not mono-exponential functions. It is shown that the commonly used Förster theory is a special case of the EFT. Strategies are presented for applying the EFT, which makes use of Brownian dynamics simulation.