Topic 195

automated user microscopy fluorescence optical imaging tracking device software affordable microscope hardware quality smartphone bioengineering time computer simple microscopes printed applications design describe field developed versatile monitoring 3d application cost tools devices controlled system manual image light introduce enabling behaving throughput interface easily parts users imagej resolution fluorescent open friendly present tetraspeck combines integrates technologies microfluidic preparation allows tool pipeline electronics advanced autofocus multiplexing handling real components care scalable lapse advances thin compatible experiments thick illumination filters over perform division focusing python robots monitor semi mesoscopy categorynew printing fluorophore dynamic automation create continuous miniaturized multiplane require practical vision beam available

32 items. Top items listed below.

Pocket MUSE: an affordable, versatile and high performance fluorescence microscope using a smartphone 195 70 18 4

Democratising "Microscopi": a 3D printed automated XYZT fluorescence imaging system for teaching, outreach and fieldwork 195 7 4

Multiplexed End-point Microfluidic Chemotaxis Assay using Centrifugal Alignment 195 18 4

The Mouse Action Recognition System (MARS): a software pipeline for automated analysis of social behaviors in mice 195 62 59 4 2

Optical spike detection and connectivity analysis with a far-red voltage-sensitive fluorophore reveals changes to network connectivity in development and disease 195 70 18 11 2

Miniaturized Devices for Bioluminescence Imaging in Freely Behaving Animals 195 70 18

Automated tracking of S. pombe spindle elongation dynamics 195 68 62 4

A benchmarking model for validation and standardization of traction force microscopy analysis tools 195 18 4

Customizable Live-Cell Imaging Chambers for Multimodal and Multiplex Fluorescence Microscopy. 195 70 18 4

Active focus stabilization for fluorescence microscopy by tracking actively generated infrared spots. 195 18 8

How to quantitatively measure, assess and correct the fluorescence crosstalk in the wide-field microscopy 195 70 18 4

Flexible open-source automation for robotic bioengineering 195 62 18 4

The XyloPhone: democratizing access to high-quality macroscopic imaging for wood and other substrates 195 18 4

A streamlined workflow for automated cryo focused ion beam milling 195 111 18 4

A practical staging atlas to study embryonic development of Octopus vulgaris under controlled laboratory conditions 195 18

Dynamic visualisation of million-tip trees: the OneZoom project 195 62 4

Low-cost 3D-printed inverted microscope to detect Mycobacterium tuberculosis in a MODS culture 195 18 15

An in-vitro BBB-on-a-chip open model of human blood-brain barrier enabling advanced optical imaging 195 70 18 7

Quantitative and dynamic cell polarity tracking in plant cells 195 16

Integrating computer-aided engineering and computer-aided design for DNA assemblies 195 85 18 4

Simultaneous monitoring of the same animals with PIT-tags and sensor nodes causes no system interference 195 30

Automated continuous evolution of proteins in vivo 195 18

Anipose: a toolkit for robust markerless 3D pose estimation 195 62 59 4

Need for speed: Examining protein behaviour during cryoEM grid preparation at different timescales 195 18

Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits 38 4

BoardION: real-time monitoring of Oxford Nanopore Technologies devices 195 62 13 4

Dragonfly Inspired Smart Soft Robot 195 85 18

An image J plugin for the high throughput image analysis of in vitro scratch wound healing assays 18 4

ChipSeg: an automatic tool to segment bacteria and mammalian cells cultured in microfluidic devices 18 4

Learned SPARCOM: Unfolded Deep Super-Resolution Microscopy 184 70 26 18 4

Automated cell tracking using StarDist and TrackMate 62 18 4

3D quantification of zebrafish cerebrovascular architecture by automated image analysis of light sheet fluorescence microscopy datasets 70 62 18 4

Dual-view light-sheet imaging through tilted glass interface using a deformable mirror 70 18 4

A fuzzy-registration approach to track cell divisions in time-lapse fluorescence microscopy 70 18 4

Combined Selective Plane Illumination Microscopy and FRAP maps intranuclear diffusion of NLS-GFP 70 18 4

anTraX: high throughput video tracking of color-tagged insects 62 4

HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data 62 4 2

OrganoidTracker: efficient cell tracking using machine learning and manual error correction 26 4

EZcalcium: Open Source Toolbox for Analysis of Calcium Imaging Data 62 59 4 2

Enhanced tissue penetration of antibodies through pressurized immunohistochemistry 195 18

Automated screening by 3D light-sheet microscopy with high spatial and temporal resolution reveals mitotic phenotypes 70 18 4

Transient Room Lighting for Ambient Light Multiphoton Microscopy 70 18 4

The Mathematics Underlying Eeg Oscillations Propagation 195 38

CellMAPtracer: A user-friendly tracking tool for long-term migratory and proliferating cells 7 4

A polymer gel index-matched to water enables diverse applications in fluorescence microscopy 70 18 8

CiliaQ - a simple, open-source software for automated quantification of ciliary morphology and fluorescence in 2D, 3D, and 4D images 62 18 4

Determining the Depth Limit of Bioluminescent Sources in Scattering Media 70 18

High-speed, long-term, 4D in vivo lifetime imaging in intact and injured zebrafish and mouse brains by instant FLIM 70 18 4

A hybrid open-top light-sheet microscope for multi-scale imaging of cleared tissues 70 18 4

Cellbow: a robust customizable cell segmentation program 26 4

BioDynaMo: an agent-based simulation platform for scalable computational biology research 62 4

Fast 3D imaging of giant unilamellar vesicles using reflected light-sheet microscopy with single molecule sensitivity 70 18 8

Semi-automatic stitching of filamentous structures in image stacks from serial-section electron tomography 59 4

Multi-Modal Single-Molecule Imaging with Continuously Controlled Spectral-resolution (CoCoS) Microscopy 70 18 8 4

Wide field-of-view volumetric imaging by a mesoscopic scanning oblique plane microscopy with switchable objective lens 70 18 7 4

GIANI: open-source software for automated analysis of 3D microscopy images 62 13 4

Multiplane Mesoscope reveals distinct cortical interactions following expectation violations 195 11 2

Computational Tool for Ensemble Averaging of Single-Molecule Data 62 18 4

A low-cost, open source, self-contained bacterial EVolutionary biorEactor (EVE) 18 4

FalseColor-Python: a rapid intensity-leveling and digital-staining package for fluorescence-based slide-free digital pathology 70 18 4

Multifocal imaging for precise, label-free tracking of fast biological processes in 3D 70 18 4

Removable cranial window for sustained wide-field optical imaging in mouse neocortex 70 18 2

An open-source experimental framework for automation of cell biology experiments 7 4

CryoSIM: super resolution 3D structured illumination cryogenic fluorescence microscopy for correlated ultra-structural imaging 70 18 8 4

TranSPHIRE: Automated and feedback-optimized on-the-fly processing for cryo-EM 111 62 4

EPySeg: a coding-free solution for automated segmentation of epithelia using deep learning 176 62 4

Frequency-independent biological signal identification (FIBSI): A free program that simplifies intensive analysis of non-stationary time series data 184 123 4

Biological network growth in complex environments - a computational framework 38 18 4

PhenoImage: an open-source GUI for plant image analysis 62 4

SpineS: An interactive time-series analysis software for dendritic spines 77 26 2

Three-Dimensional Label-Free Imaging and Quantification of Migrating Cells during Wound Healing 70 18 4

Development of an objective index, neural activity score (NAS), reveals neural network ontogeny and treatment effects on microelectrode arrays 4 2

TRex, a fast multi-animal tracking system with markerless identification, 2D body posture estimation and visual field reconstruction 62 30 4

Single-molecule light-sheet microscopy with local nanopipette delivery 70 18 8

Bi-channel Image Registration and Deep-learning Segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain 62 26 4 2

ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data 176 62 4

A low-cost smart system for electrophoresis-based nucleic acids detection at the visible spectrum 18 4

A knock-in Drosophila model supports a conserved link between potassium channelopathy and involuntary movement 195 82

PartSeg, a Tool for Quantitative Feature Extraction From 3D Microscopy Images for Dummies 62 4

Optimization of negative stage bias potential for faster imaging in large-scale electron microscopy 70 18 4

CorRelator: An interactive and flexible toolkit for high-precision cryo-correlative light and electron microscopy 62 13 4

Online analysis of microendoscopic 1-photon calcium imaging data streams 59 4 2

3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy 111 18 4

TaxisPy: A Python-based Software for the Quantitative Analysis of Bacterial Chemotaxis 62 4

Open source software tool for the automated detection and characterization of epithelial cells from trace biological samples 18 4

YeaZ: A convolutional neural network for highly accurate, label-free segmentation of yeast microscopy images 26 4

Virtual-SMLM, a virtual environment for real-time interactive SMLM acquisition 62 18 4

The DMCdrive: practical 3D-printable micro-drive system for reliable chronic multi-tetrode recording and optogenetic application in freely behaving rodents 50 11 2

μCB-seq: Microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells 43 18 4

A simple Ca2+-imaging approach to neural network analysis in cultured neurons 18 4 2

Fluorescence Microscopy Datasets for Training Deep Neural Networks 26 4

Label-free and Multimodal Second Harmonic Generation Light Sheet Microscopy 70 18 4

A deep learning algorithm for 3D cell detection in whole mouse brain image datasets 70 18 11 4

Probabilistic Approach to Understand Errors in Sequencing and its based Applications 145 4

FRC-QE: A robust and comparable 3D microscopy image quality metric for cleared organoids 70 18 4

HPM Live μ for full CLEM workflow 70 18 4

A head-fixation system for continuous monitoring of force generated during behavior 23 2

μSPIM: A Software Platform for Selective Plane Illumination Microscopy 70 18 4

DeepCINAC: a deep-learning-based Python toolbox for inferring calcium imaging neuronal activity based on movie visualization 26 4 2

A Wi-Fi live streaming Centrifuge Force Microscope for benchtop single-molecule experiments 18 4