Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Automating multimodal microscopy with NanoJ-Fluidics.

ABSTRACT: Combining and multiplexing microscopy approaches is crucial to understand cellular events, but requires elaborate workflows. Here, we present a robust, open-source approach for treating, labelling and imaging live or fixed cells in automated sequences. NanoJ-Fluidics is based on low-cost Lego hardware controlled by ImageJ-based software, making high-content, multimodal imaging easy to implement on any microscope with high reproducibility. We demonstrate its capacity on event-driven, super-resolved live-to-fixed and multiplexed STORM/DNA-PAINT experiments.

SUBMITTER: Almada P

PROVIDER: S-EPMC6420627 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Automating multimodal microscopy with NanoJ-Fluidics.

Almada Pedro P Pereira Pedro M PM Culley Siân S Caillol Ghislaine G Boroni-Rueda Fanny F Dix Christina L CL Charras Guillaume G Baum Buzz B Laine Romain F RF Leterrier Christophe C Henriques Ricardo R

Nature communications 20190315 1

Combining and multiplexing microscopy approaches is crucial to understand cellular events, but requires elaborate workflows. Here, we present a robust, open-source approach for treating, labelling and imaging live or fixed cells in automated sequences. NanoJ-Fluidics is based on low-cost Lego hardware controlled by ImageJ-based software, making high-content, multimodal imaging easy to implement on any microscope with high reproducibility. We demonstrate its capacity on event-driven, super-resolv ...[more]

PMID: 30874553

Similar Datasets

An open source 16-channel fluidics system for automating sequential fluorescent <i>in situ</i> hybridization (FISH)-based imaging.

Project description:Fluorescent in situ hybridization (FISH) can provide spatial information about DNA/RNA targets in fixed cells and tissues. However, the workflows of multiplexed FISH-based imaging that use sequential rounds of hybridization quickly become laborious as the number of rounds increases because of liquid handling demands. Here, we present an open-source and low-cost fluidics system that is purpose built for automating the workflows of sequential FISH-based imaging. Our system features a fluidics module with 16 addressable channels in which flow is positive pressure-driven and switched on/off by solenoid valves in order to transfer FISH reagents to the sample. Our system also includes a controller with a main printed circuit board that can control up to 120 solenoid valves and allows users to control the fluidics module via serial communication. We demonstrate the automatic and robust fluid exchange with this system by targeting the alpha satellite repeat in HeLa cell with 14 rounds of sequential hybridization and imaging. We anticipate that this simple and flexible system will be of utility to researchers performing multiplexed in situ assays in a range of experimental systems.

| S-EPMC9358477 | biostudies-literature

mmSTORM: Multimodal localization based super-resolution microscopy.

Project description:Super-resolution localization microscopy provides a powerful tool to study biochemical mechanisms at single molecule level. Although the lateral position of the fluorescent dye molecules can be determined routinely with high precision, measurement of other modalities such as 3D and multicolor without the degradation of the original super-resolved image is still in the focus. In this paper a dual-objective multimodal single molecule localization microscopy (SMLM) technique has been developed, optimized and tested. The proposed optical arrangement can be implemented onto a conventional inverted microscope without serious system modification. The performance of the method was tested using fluorescence beads, F-actin filaments and sarcomere structures. It was shown that the proposed imaging method does not degrade the image quality of the original SMLM 2D image but could provide information on the axial position or emission spectra of the dye molecules.

| S-EPMC6349879 | biostudies-literature

Multimodal CARS microscopy of structured carbohydrate biopolymers.

Project description:We demonstrate the utility of multimodal coherent anti-Stokes Raman scattering (CARS) microscopy for the study of structured condensed carbohydrate systems. Simultaneous second-harmonic generation (SHG) and spectrally-scanned CARS microscopy was used to elucidate structure, alignment, and density in cellulose cotton fibers and in starch grains undergoing rapid heat-moisture swelling. Our results suggest that CARS response of the O-H stretch region (3000 cm(-1)-3400 cm(-1)), together with the commonly-measured C-H stretch (2750 cm(-1)-2970 cm(-1)) and SHG provide potentially important structural information and contrast in these materials.

| S-EPMC3018121 | biostudies-other

Automating ALCHEMI at the nano-scale using software compatible with PC-controlled transmission electron microscopy

Project description:A software-control system has been developed that enables access to site-selective energy-dispersive X-ray spectroscopy/electron energy-loss spectroscopy measurements from a sub-micrometre area by automatically and concurrently tilting the beam and acquiring spectra. Atom location by channeling-enhanced microanalysis (ALCHEMI) is a technique to obtain atom-site-specific information on constituent elements in a crystalline sample by acquiring a set of core electron transition spectra while tilting the incident beam. This methodology has been extended to a more quantitative technique called high-angular-resolution electron-channeled X-ray/electron spectroscopy (HARECXS/HARECES). There is a growing demand for analyzing smaller areas, such as small particles and multilayers. However, the minimum size of a region of interest probed by the present hardware-assisted automated HARECXS/HARECES scheme is limited to no smaller than 1 µm, not only by the size of the electron probe and its convergence angle but also by the movement of the probe position associated with the beam tilt due to aberrations of the hardware system. Herein, QED (quantitative electron diffraction), a commercial plug-in working on an integrated software platform, Gatan Microscopy Suite, was modified to enable the calibration and control of the probe to resolve the aforementioned limitation. In addition, a more sophisticated scheme for QED was developed to realize the ALCHEMI method for energy-dispersive X-ray spectroscopy, electron energy-loss spectroscopy or both concurrently. This allows access to ALCHEMI and its derivative methods, automatically executed with any type of current PC-controlled commercial microscope on an area as small as 30 nm, without modifying the hardware system.

| S-EPMC9172042 | biostudies-literature

A fluidics-based impact sensor.

Project description:Microelectromechanical systems (MEMS)-based high-performance accelerometers are ubiquitously used in various electronic devices. However, there is an existing need to detect physical impacts using low-cost devices with no electronic circuits or a battery. We designed and fabricated an impact sensor prototype using a commercial stereolithography apparatus that only consists of a plastic housing and working fluids. The sensor device responds to the instantaneous acceleration (impact) by deformation and pinch off of a water droplet that is suspended in oil in a sensor cavity. We tested the various geometrical and physical parameters of the impact sensor to identify their relations to threshold acceleration values. We show that the state diagram that is plotted against the dimensionless Archimedes and Bond numbers adequately describes the response of the proposed sensor.

| S-EPMC5892937 | biostudies-literature

Multimodal microscopy for automated histologic analysis of prostate cancer.

Project description:BackgroundProstate cancer is the single most prevalent cancer in US men whose gold standard of diagnosis is histologic assessment of biopsies. Manual assessment of stained tissue of all biopsies limits speed and accuracy in clinical practice and research of prostate cancer diagnosis. We sought to develop a fully-automated multimodal microscopy method to distinguish cancerous from non-cancerous tissue samples.MethodsWe recorded chemical data from an unstained tissue microarray (TMA) using Fourier transform infrared (FT-IR) spectroscopic imaging. Using pattern recognition, we identified epithelial cells without user input. We fused the cell type information with the corresponding stained images commonly used in clinical practice. Extracted morphological features, optimized by two-stage feature selection method using a minimum-redundancy-maximal-relevance (mRMR) criterion and sequential floating forward selection (SFFS), were applied to classify tissue samples as cancer or non-cancer.ResultsWe achieved high accuracy (area under ROC curve (AUC) >0.97) in cross-validations on each of two data sets that were stained under different conditions. When the classifier was trained on one data set and tested on the other data set, an AUC value of ~0.95 was observed. In the absence of IR data, the performance of the same classification system dropped for both data sets and between data sets.ConclusionsWe were able to achieve very effective fusion of the information from two different images that provide very different types of data with different characteristics. The method is entirely transparent to a user and does not involve any adjustment or decision-making based on spectral data. By combining the IR and optical data, we achieved high accurate classification.

| S-EPMC3045985 | biostudies-literature

Multimodal single-molecule microscopy with continuously controlled spectral resolution.

Project description:Color is a fundamental contrast mechanism in fluorescence microscopy, providing the basis for numerous imaging and spectroscopy techniques. Building on spectral imaging schemes that encode color into a fixed spatial intensity distribution, here, we introduce continuously controlled spectral-resolution (CoCoS) microscopy, which allows the spectral resolution of the system to be adjusted in real-time. By optimizing the spectral resolution for each experiment, we achieve maximal sensitivity and throughput, allowing for single-frame acquisition of multiple color channels with single-molecule sensitivity and 140-fold larger fields of view compared with previous super-resolution spectral imaging techniques. Here, we demonstrate the utility of CoCoS in three experimental formats, single-molecule spectroscopy, single-molecule Förster resonance energy transfer, and multicolor single-particle tracking in live neurons, using a range of samples and 12 distinct fluorescent markers. A simple add-on allows CoCoS to be integrated into existing fluorescence microscopes, rendering spectral imaging accessible to the wider scientific community.

| S-EPMC9680784 | biostudies-literature

The role of altered lipid composition and distribution in liver fibrosis revealed by multimodal nonlinear optical microscopy

Project description:To reveal the involved gene regulatory pathways, we carried out RNA-seq transcriptomics analysis on the cells treated with or without PA, treated with PA+OA and PA+BMS.

2022-12-22 | GSE220856 | GEO

DNA Assembly in 3D Printed Fluidics.

Project description:The process of connecting genetic parts-DNA assembly-is a foundational technology for synthetic biology. Microfluidics present an attractive solution for minimizing use of costly reagents, enabling multiplexed reactions, and automating protocols by integrating multiple protocol steps. However, microfluidics fabrication and operation can be expensive and requires expertise, limiting access to the technology. With advances in commodity digital fabrication tools, it is now possible to directly print fluidic devices and supporting hardware. 3D printed micro- and millifluidic devices are inexpensive, easy to make and quick to produce. We demonstrate Golden Gate DNA assembly in 3D-printed fluidics with reaction volumes as small as 490 nL, channel widths as fine as 220 microns, and per unit part costs ranging from $0.61 to $5.71. A 3D-printed syringe pump with an accompanying programmable software interface was designed and fabricated to operate the devices. Quick turnaround and inexpensive materials allowed for rapid exploration of device parameters, demonstrating a manufacturing paradigm for designing and fabricating hardware for synthetic biology.

| S-EPMC4699221 | biostudies-literature

Accelerating Enzymatic Catalysis Using Vortex Fluidics.

Project description:Enzymes catalyze chemical transformations with outstanding stereo- and regio-specificities, but many enzymes are limited by their long reaction times. A general method to accelerate enzymes using pressure waves contained within thin films is described. Each enzyme responds best to specific frequencies of pressure waves, and an acceleration landscape for each protein is reported. A vortex fluidic device introduces pressure waves that drive increased rate constants (kcat ) and enzymatic efficiency (kcat /Km ). Four enzymes displayed an average seven-fold acceleration, with deoxyribose-5-phosphate aldolase (DERA) achieving an average 15-fold enhancement using this approach. In solving a common problem in enzyme catalysis, a powerful, generalizable tool for enzyme acceleration has been uncovered. This research provides new insights into previously uncontrolled factors affecting enzyme function.

| S-EPMC5524626 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data