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An adaptive excitation source enables two- and three-photon imaging of the awake mouse brain with high spatial and temporal resolution at 30-fold-reduced laser power relative to conventional approaches.
The 2018 Human Protein Atlas Image Classification competition sought to improve automated classification of protein subcellular localizations from fluorescence images. The winning strategies involved innovative deep learning approaches for multi-label classification.
The unique advantages of single-particle cryo-electron microscopy and cryo-electron tomography are combined in a method called TYGRESS, here applied to determine the structure of the intact ciliary axoneme at a resolution of 12 Å.
An approach combining cryo-electron microscopy and mass spectrometry analysis of protein complexes enriched directly from cells enables structure determination of unknown complexes at atomic resolution.
Single-cell isolation following time-lapse imaging (SIFT) enables high-throughput screening of complex and dynamic phenotypes from pooled bacterial libraries. SIFT was used to generate ultraprecise synthetic gene oscillators.
A new method of autophagy measurement is based on the detection of phospho-ATG16L1, a conserved early marker of autophagy. Sensitive detection can be achieved in multiple biological systems and assays with advantages over standard methods.
A miniaturized NMR-on-a-chip needle can be implanted into rodent brains and can measure blood flow and oxygenation changes in vivo in a small volume at an unprecedentedly high temporal resolution of a few milliseconds.
DuMPLING (dynamic μ-fluidic microscopy phenotyping of a library before in situ genotyping) enables screening of dynamic phenotypes in strain libraries and was used here to study genes that coordinate replication and cell division in Escherichia coli.
Probabilistic cell typing by in situ sequencing (pciSeq), leverages previous single-cell RNA sequencing classification and multiplexed in situ RNA detection to spatially map cell types accurately in the mouse hippocampus and isocortex.
An alternative to focused ion beam scanning electron microscopy (FIB-SEM), gas cluster ion beam scanning electron microscopy (GCIB-SEM) is compatible with large tissue samples while achieving similar isotropic resolution.
VarID is a computational method that quantifies the dynamics of transcriptional variability with the goal of identifying the role of highly variable genes, such as weakly expressed transcription factors, in cell differentiation or state transitions.
Micropatterning of cryo-EM grids enables controlled adhesion of mammalian cells for cryo-ET-based structural studies. This approach leads to reproducible cellular morphology and improves focused ion beam thinning of cells for in-cell structural analyses.
FreeHi-C takes Hi-C sequencing data as input and simulates reads with random mutations and indels from the interacting fragment pairs. FreeHi-C-simulated replicates are used for benchmarking Hi-C analysis methods and enable data augmentation for differential chromatin interaction analysis.
Tissue fixation with formaldehyde and a water-soluble carbodiimide crosslinker (EDC) leads to retention of extracellular vesicles within tissues and allows for reliable extracellular vesicle imaging for semiquantitative imaging applications.
Deep-Z uses deep learning to go from a two-dimensional snapshot to three-dimensional fluorescence images. The method improves imaging speed while reducing light dose, and was shown to be useful for accurate structural and functional imaging of neurons in Caenorhabditis elegans.
mmvec, a neural-network-based algorithm, uses paired multiomics data (microbial sequence counts and metabolite abundances) to compute the conditional probability of observing a metabolite in the presence of a specific microorganism.
One third of verified gene knock outs with CRISPR still show residual protein expression owing to translation reinitiation or exon skipping. Several proteins are still functional. The authors call for a systematic analysis of protein levels after genome editing.
The 2018 Data Science Bowl challenged competitors to develop an accurate tool for segmenting stained nuclei from diverse light microscopy images. The winners deployed innovative deep-learning strategies to realize configuration-free segmentation.
Seamless integration of single-molecule localization microscopy and STED allows for correlative live imaging of protein position and movement at the nanoscale in the context of fine morphological features.
Optobodies combine split intracellular antibodies (intrabodies) with light-controlled dimerization tools for spatiotemporal control of intrabody activity. The developed tools demonstrate the versatility and power of this approach for probing protein function.
Cellular lipids, labeled with a charged reporter, yield characteristic MS1 and MS2 patterns during mass spectrometry. These reporters allow sample multiplexing and sensitive detection of lipid metabolism at single cell resolution.
An integrated pipeline for processing cryo-ET data implemented in EMAN2 streamlines data processing to minimize human bias, and improves the quality and resolution of resulting macromolecular structures, both in vitro and in cells.
SAUCIE, a deep learning platform to analyze single-cell data across samples and platforms, allows information to be obtained from the internal layers of the network, which provides additional mechanistic understanding that can be used to further tune data analysis.
DNA-PAINT is sped up by an order of magnitude by optimizing sequences and buffer conditions, enabling faster imaging with no compromise to image quality or resolution, improved single-molecule counting and enhanced cellular imaging.
The challenge of accurate particle picking in cryo-EM analysis is addressed with Topaz, a neural-network-based algorithm that shows advantages over other tools, especially in picking unusually shaped particles.
Fiber photometry with tapered fibers allows monitoring of neural activity in larger volumes than with flat-cleaved fibers. In addition, signals from different depths can be resolved with the same tapered fiber.
SCAPE 2.0 is a versatile imaging platform that enables real-time three-dimensional microscopy of cellular function and dynamic motion in living organisms at over 100 volumes per second with minimal photodamage, and high-throughput structural imaging in fixed, cleared and expanded samples.
Cell lines in which Nup96 is endogenously tagged with mEGFP, SNAP-tag, HaloTag or mMaple serve as versatile reference samples, enabling 3D resolution calibration, assessment of labeling efficiency and precise molecular counting.
Phase plates improve contrast in cryo-electron microscopy, but suffer from electrostatic charging and electron scattering. A laser phase plate overcomes these problems and may improve imaging of biological specimens.