Advanced Fluorescence Microscopy Techniques

FRAME-tags: genetically encoded fluorescent markers for multiplexed barcoding and time-resolved tracking of live cells

The paper introduces FRAME-tags, genetically encoded fluorescent barcodes that enable scalable and time-resolved tracking of live cells using unique FP expression ratios.

Neural Anatomy and Optical Microscopy (NAOMi) Simulation for evaluating calcium imaging methods

The paper introduces NAOMi, a simulation framework for evaluating calcium imaging methods using in silico mouse cortex data, comparing segmentation algorithms and optical designs.

Focus-tunable microscope for imaging small neuronal processes in freely moving animals

The paper introduces a miniature 1-photon microscope with tunable focus for imaging fine neuronal structures in freely moving mice during behavioral tasks.

Large-scale voltage imaging in the brain using targeted illumination

This paper demonstrates targeted illumination with SomArchon to enable large-scale voltage imaging in the brain, improving signal contrast and reducing background contamination.

A genetically encoded GRAB sensor for measuring serotonin dynamics in vivo

This paper develops a genetically encoded sensor to measure serotonin dynamics in vivo, showing its effectiveness in both flies and mice across various conditions.

High fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging in vivo

This paper introduces a method to accurately estimate spikes and subthreshold waveforms from 1-photon voltage imaging in vivo, even with noise.

An optimized tissue clearing protocol for rat brain labeling, imaging, and high throughput analysis

The paper introduces an optimized tissue clearing protocol for rat brains and develops an open-source platform for high-throughput analysis.

Targeted volumetric single-molecule localization microscopy of defined presynaptic structures in brain sections

The paper develops a method for 3D-dSTORM imaging of mouse brain sections to analyze presynaptic active zones, finding differences in Bassoon cluster size and density across hippocampal regions.

Open-top axially swept light sheet microscopy

This paper introduces OTAS-LSM, a high-throughput microscopy technique with improved axial resolution for imaging optically cleared tissues at the single-cell level.

Improving the flexibility of Genetically Encoded Voltage Indicators via intermolecular FRET

The paper develops a new family of GEVIs using intermolecular FRET, showing larger voltage-dependent signals and improved cell type specificity.

High-resolution two-photon transcranial imaging of brain using direct wavefront sensing

This paper develops adaptive optics two-photon microscopy to achieve high-resolution transcranial imaging of brain neurons in living mice.

Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice

The paper characterizes the relationship between spiking activity and fluorescence signals in GCaMP6-expressing neurons, finding GCaMP6s has better single-spike detection than GCaMP6f.

Freeze-frame imaging of dendritic calcium signals with TubuTag

This paper introduces TubuTag, a genetically encoded calcium sensor for imaging dendritic calcium signals in neurons with high temporal and spatial resolution.

TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data

TRAIT2D is a Python software for analyzing single particle diffusion data, offering tracking, analysis, and simulation with a graphical interface.

A Fast High-Affinity Fluorescent Serotonin Biosensor Engineered from a Tick Lipocalin

The authors retracted their paper due to irreproducible results and contamination issues in their experimental materials.

Split-wrmScarlet and split-sfGFP: Tools for faster, easier fluorescent labeling of endogenous proteins in Caenorhabditis elegans

The paper introduces split-wrmScarlet and split-sfGFP tools for faster fluorescent labeling of endogenous C. elegans proteins using CRISPR.

Single cell analysis of population-wide nuclear and cytosolic drug responses using high-content FRET imaging: measuring protein kinase activation in rat primary striatal neurons

The paper uses single-cell FRET imaging to analyze drug-induced signaling responses in rat neurons, revealing significant intercellular variation not detectable by bulk methods.

Online analysis of microendoscopic 1-photon calcium imaging data streams

This paper introduces two online algorithms for real-time analysis of microendoscopic calcium imaging data, improving computational efficiency and enabling closed-loop experiments.

PICASSO: Ultra-multiplexed fluorescence imaging of biomolecules through single-round imaging and blind source unmixing

PICASSO enables ultra-multiplexed fluorescence imaging of biomolecules through single-round imaging and blind source unmixing, achieving over 15-color multiplexing in various applications.

Algorithms for the selection of fluorescent reporters

The paper presents algorithms and an open-source tool to optimize fluorophore panels for maximal signal and minimal bleed-through in fluorescent measurements.

Application of Airy beam Light sheet microscopy to examine early neurodevelopmental structures in 3D hiPSC-derived human cortical spheroids

This paper optimizes Airy-beam light sheet microscopy to image 3D structures in hiPSC-derived human cortical spheroids, enabling high-resolution analysis of neurodevelopmental processes.

Repeat DNA-PAINT suppresses background and non-specific signals in optical nanoscopy

The paper introduces Repeat DNA-PAINT, a method that reduces background and non-specific signals in DNA-PAINT by lowering imager concentration, while maintaining spatial resolution.

Large-scale calcium imaging with a head-mount axial scanning 3D fluorescence microscope

This paper develops a 3D fluorescence microscope and algorithm to image more neurons in freely behaving mice compared to 2D methods.

Large-scale cellular-resolution imaging of neural activity in freely behaving mice

This paper introduces a novel miniaturized mesoscope for cellular-resolution imaging of neural activity in freely behaving mice, enabling comprehensive visualization across brain regions.

A Simple Method for Getting Standard Error on the Ratiometric Calcium Estimator

The paper introduces a simpler method to estimate standard errors for ratiometric calcium estimators by using uncertainty propagation and Monte-Carlo methods, avoiding complex protocols and background models.

Rapid 3D-STORM imaging of diverse molecular targets in tissue

RAIN-STORM enables rapid 3D nanoscale imaging of multiple molecular targets in tissue, revealing detailed structures in human samples.

pMAT: An Open-Source Software Suite for the Analysis of Fiber Photometry Calcium Imaging

The paper introduces pMAT, an open-source software suite for analyzing fiber photometry calcium imaging data, addressing the lack of standardized analysis pipelines.

Improved genetically encoded near-infrared fluorescent calcium ion indicators for in vivo imaging

The paper introduces two improved near-infrared calcium indicators for better neuronal activity imaging in vivo.

High throughput instrument to screen fluorescent proteins under two-photon excitation

The paper introduces a high-throughput instrument called GIZMO to screen fluorescent protein mutants under two-photon excitation, enabling efficient evolution of proteins optimized for this excitation method.

Deep ultraviolet light based wide-field fluorescence microscope for brain imaging

This paper describes a deep ultraviolet light-based wide-field fluorescence microscope for 2D and 3D brain imaging, demonstrating its versatility and applicability for rodent brain studies.