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opencc-by-4.0Aug 2024View details →

Rapid Identification of Bacterial isolates Using Microfluidic Adaptive Channels and Multiplexed Fluorescence Microscopy

Dataset for: Rapid Identification of Bacterial isolates Using Microfluidic Adaptive Channels and Multiplexed Fluorescence Microscopy doi: <a title="Link to landing page via DOI" href="https://doi.org/10.1039/D4LC00325J">10.1039/D4LC00325J</a>

opencc-by-4.0Jan 2020View details →

Probiotic Bacillus subtilis Protects against a-Synuclein Aggregation in C. elegans (fluorescence microscopy data)

This project has been submitted by the Maria Doitsidou Lab. Project contents: This project contains datasets of z-stack images of C. elegans strains used to study how the gut microbiome affects Parkinson’s disease. Each strain contains a chromosomal insertion containing YFP fused to α-synuclein (pkIs2386[Punc-54::α-synuclein::YFP + unc-119(+)]). The following C. elegans strains were used and/or created for this project: NL5901 pkIs2386[Punc-54::α-synuclein::YFP + unc-119(+)] MDH586 daf-2(e1370) III; pkIs2386 MDH585 daf-16(mu86) I; pkIs2386 MDH587 hsf-1(sy441) I; pkIs2386 MDH657 daf-2(e1370) III; daf-16(mu86) I; pkIs2386 MDH614 daf-2(gk390525) III; pkIs2386 MDH611 eat-2(ad465) II; pkIs2386 MDH711 lagr-1(gk331) I, pkIs2386 MDH725 sptl-3(ok1927) II; pkIs2386 MDH724 asm-3(ok1744) IV; pkIs2386. High magnification (40x objective) z stack images of the head region were obtained by using a Zeiss Axio imager 2 microscope. Aim: Study how a probiotic B. subtilis strain affects alpha-synuclein protein aggregation. Main results: The authors showed that the probiotic B. subtilis strain PXN21 inhibits and clears a-synuclein aggregation in a C. elegans model. The bacterium acts via metabolites and biofilm formation to activate protective pathways in the host, including DAF-16/FOXO and sphingolipid metabolism. Contributors: Maria Eugenia Goya, Feng Xue, Cristina Sampedro-Torres-Quevedo, Sofia Arnaouteli, Lourdes Riquelme-Dominguez, Andres Romanowski, Jack Brydon, Kathryn L. Ball, Nicola R. Stanley-Wall and Maria Doitsidou These datasets were used in the following publication: Probiotic Bacillus subtilis Protects against a-Synuclein Aggregation in C. elegans Maria Eugenia Goya, Feng Xue, Cristina Sampedro-Torres-Quevedo, Sofia Arnaouteli, Lourdes Riquelme-Dominguez, Andres Romanowski, Jack Brydon, Kathryn L. Ball, Nicola R. Stanley-Wall and Maria Doitsidou Cell Reports January 14, 2020 30 367-380; first published January 14, 2020 <a href="https://doi.org/10.1016/j.celrep.2019.12.078">https://doi.org/10.1016/j.celrep.2019.12.078</a>

opencc-by-4.0May 2023View details →

fluorescence microscopy image containing more than 65536 cells

1. A montage of fluorescence images containing more than 65536 cells. 2. The output label image from Cellpose, as obtained from the BIOP Cellpose wrapper

opencc-by-4.0Sep 2023View details →

Confocal microscopy imaging of FocalCheck fluorescent beads at various oil indices under ambient temperature

the dataset consisting of 20 fields of images with physical dimensions of 1340x1340x64 pixels. These images were acquired using two different refractive indices: one with oil immersion corrected for a temperature of 23°C and another with oil immersion corrected for a temperature of 37°C. A constant temperature of 24.5°C was maintained throughout the data collection

dryad36/100

Deep learning-based autofocus method enhances image quality in light-sheet fluorescence microscopy

Open the record for dataset details and reuse information.

publicSep 2025View details →

opencc-by-4.0Oct 2020View details →

Raw data accompanying the manuscript "Super-resolution fluorescence microscopy by line-scanning with an unmodified two-photon microscope"

Raw data sets (.tif files) of data utilized to demonstrate 2D SIM with an unmodified multi photon intravital fluorescence microscope.

opencc-by-4.0Nov 2016View details →

Confined diffusion of nanoparticles inserted into a diblock polymer membrane captured by fluorescence microscopy

The membrane average pore size was 1µm with a standard deviation of 0.25µm. The video was record by 50 FPS. For more information please see Haramagatti CR, Schacher FH, Müller AHE, Köhler J. Diblock copolymer membranes investigated by single-particle tracking. Phys Chem Chem Phys. 2011;13(6):2278–2284. doi:10.1039/c0cp01658f

opencc-by-4.0May 2017View details →

Fluorescence microscopy of Chlamydomonas reinhardtii for mCherry detection: secretion peptides strains.

Overview Life-cell imaging was performed with a confocal fluorescence microscopy to observe mCherry in the secretion vacuoles. mCherry fluorescence compartmentalization was observed by a Confocal Zeiss LSM 780-NLO, using an argon laser 543 nm to excite mCherry and a spectral detector set approximately to 610-650 nm range. For chlorophyll, we used a laser at 405 nm for excitation, and spectral detector set to 680 nm region. All pictures were taken with the same system configuration and analyzed by Fiji, an ImageJ distribution software. Cells images were acquired in bundles of 0.4 μm afar photos per channel in the z-axis.    Files info: Each file is the raw image obtained from fluorescent microscopy.   Organization Construct_name.czi - Ex: "pAH04mCherry.czi" pAH04mCherry -> construct without signal peptide pJP22mCherry -> construct with signal peptide from arylsulfatase 1 (Chlamydomonas reinhardtii) pJP26mCherry -> construct with signal peptide from binding protein 1 (C. reinhardtii) pJP28mCherry -> construct with signal peptide from carbonic anhydrase 1 (C. reinhardtii) pJP29 mCherry -> construct with signal peptide from ice-binding protein 1 (Artic Chlamydomonas sp) pJP30-35mCherry -> construct with signal peptide from in silico identified list (DOI 10.5281/zenodo.556792). Wildtype cc1690 -> parental strain used for transformation.   For more information on the constructs, check our paper.    Consider citing our work.  Molino JVD, de Carvalho JCM, Mayfield SP (2018) Comparison of secretory signal peptides for heterologous protein expression in microalgae: Expanding the secretion portfolio for Chlamydomonas reinhardtii. PLoS ONE 13(2): e0192433. https://doi.org/10.1371/journal. pone.0192433

opencc-by-4.0Apr 2024View details →

Localization of protoporphyrin IX in glioma patients with paired stimulated Raman histology and two-photon 3 excitation fluorescence microscopy

<div> <div> <div> <h1>Spatially resolved transcriptomics</h1> Tissue fixation was performed following the ‘Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols’ (CG000160 | Rev C), which included heating the slide and immersing it in pre-chilled methanol. In the tissue staining phase, isopropanol was applied to tissue sections followed by a series of air-drying, hema- toxylin application, washing, bluing buffer application, eosin mix addition, and further washing. The slide was then dried on a heating block. Imaging was conducted using the Evos microscope, with the settings following the previously described protocol. Permeabilization and reverse transcription were undertaken without a preceding tissue optimization on Visium Tissue Optimization Slides, as the optimal permeabiliza- tion time for brain tissue had been established at 12 minutes by a previous researcher. The overall library preparation adhered to the ‘Visium Spatial Gene Expression Reagent Kits – User Guide’ (CG000239 | Rev F). During permeabilization, the Visium slide with stained tissue sections was fitted into a slide cassette and exposed to permeabilization enzyme, followed by a wash with 0.1X SSC buffer. For reverse transcription, an RT master mix was dispensed into each well, followed by a 45-minute incubation period in a thermocycler at 53 ° Celsius. In the second strand synthesis stage, each well received an addition of 75 ul 0.08 M KOH, followed by a brief room-temperature incubation. Subsequently, wells were washed with buffer EB and re- ceived the second strand mix, before undergoing a 15-minute incubation at 65 ° Celsius in a thermocycler. The denaturation process involved washing the wells with buffer EB and adding 35 ul 0.08 M KOH in each well, which were then incubated at room temperature. Afterward, Tris 1 M pH 7.0 was pipetted into four tubes of an 8-tube strip, followed by a transfer of samples from each well into these tubes. The tubes were then vortexed, centrifuged, and placed on ice, with the remaining sample stored for subsequent stages. The experiment initiated with the determination of cycle number wherein a qPCR mix was allocated across five wells of a qPCR plate, with a negative control included. The ensuing qPCR and Cq determination followed the standard protocol used for FFPE methods. Notably, uneven Cq values starting from n.5 were rounded up. In the subsequent cDNA amplification phase, an amplification mix was introduced to each sample tube, followed by thermo-cycling for actual PCR using a specified protocol. The cDNA cleanup process involved adding a SPRIselect reagent to each sample tube, followed by a series of incubation, washing, drying, and buffer addition steps. The cleaned-up samples were then transferred to new tubes. Finally, cDNA quality control and quantification were performed using a Tape Station. The total cDNA yield was calculated, factoring in the library concentration and elution volume. The process of fragmentation, end repair, and A-tailing started with using just a quarter of the purified library, with the remaining portion stored at -20 ° Celsius. The selected volume was mixed with buffer EB and fragmentation mix and incubated in a thermal cycler. Double-sided size selection was performed to discard large fragments and retain fragments within the desired size range. This involved the use of SPRIselect reagent, and resulted in a library with reduced total volume and a smaller range of fragment sizes. Adaptor ligation involved mixing adaptor ligation mix with each sample and incubating in a thermocycler. Post-ligation cleanup followed the cleanup steps post-cDNA amplification, with minor adjustments to the quantities of SPRIselect reagent and buffer EB. Sample index PCR was then performed, with an amp mix and dual index TT set A added to each sample, followed by a specific PCR protocol. The total number of cycles was determined based on the cDNA yield. Another round of double-sided size selection was performed, this time with varied substance quantities, to ensure another cleanup stage. The process concluded with a post-library construction quality control, ensuring the success of the library construction. While no exact concentration calculations were necessary, the fragment size in base pairs was of interest. A Fragment Analyzer was used due to its availability and accuracy in fragment size calculation. Sequencing was performed on a NextSeq 550. <h1>Postprocessing and analysis pipeline</h1> The data analysis and quality control for this research was conducted using the 10X Genomics’ space ranger pipeline and the SPATA2 (version 2.0) framework for spatial data analysis. The SPATA2 object was initiated through the ‘SPATA2::initiateSpataObject_10X’ function. This import procedure involved several stages using the Seurat version 4.0 package. Firstly, gene expression normalization was performed by dividing each spot’s values by the estimated total number of transcripts. These normalized values were then multiplied by 10,000 and underwent a natural logarithm transformation to improve interpretability and comparability across genes. Next, a regression model was applied to remove batch effects and scale the data. This model factored in sample batch and the expression percentages of ribosomal and mitochondrial genes, helping to control for potential sources of unwanted variation in the data. For a more detailed understanding of this process, you can refer to the guide provided at this link: https://themilolab.github.io/SPATA2/. This guide provides comprehensive information about the SPATA2 package and its application in spatial transcriptomics analysis. </div> </div> </div> <div> <div> <div> <h1>Postprocessing and imaging analysis</h1> The H&E images along with the PpIX and SRH images were aligned using afine transformation as described recently. For classification of the PpIX patterns we extracted 160x160 sized patches from each barcode spot and predicted the pattern using the pretrained ResNet architecture. </div> </div> </div>

FIGURE 6 in Devonian smooth-walled tasmanids and new insights of life-cycle descriptions through fluorescence microscopy

FIGURE 6. Life stage interpretative drawings based off of interpretation schematic of modern marine algal cysts (Bravo and Figueroa, 2014). 6a: image of tasmanid in a vegetative stage; 6b: image of a tasmanid in a gamete sack stage; 6c image of a tasmanid in a dividing cyst stage; 6d: image of a tasmanid in a resting cyst stage.

FIGURE 3 in Devonian smooth-walled tasmanids and new insights of life-cycle descriptions through fluorescence microscopy

FIGURE 3. Transmitted and incident light images of silica-rich microspherules retrieved from the Oatka Creek Formation, Leroy, New York. 1a–c conjoined or splitting tasmanid containing internal pyritic inclusions, interpreted to be a dividing cyst; 2a–c single tasmanid with no pyritic inclusions but numerous surficial punctae, interpreted to be a vegetative cyst; 3a–c tasmanid with well defined internal structure interpreted to be a resting cyst. Images taken at a magnification of 10x, average diameter of all cysts, 125 µm.

FIGURE 2 in Devonian smooth-walled tasmanids and new insights of life-cycle descriptions through fluorescence microscopy

FIGURE 2. Transmitted and incident light images of silica-rich microspherules retrieved from the Oatka Creek Formation, Leroy, New York. Internal to external (left to right) focal point shift imaging approach allows for internal structures at different points within the tasmanid to be imaged: 1a–e: internal pyritic inclusions imaged throughout single tasmanid, inclusions interpreted to be portions of gamete stage internal strucres; 2a–e, surface punctae visible (2a) in addition to internal pyritic inclusions; 3 a–e conjoined or splitting tasmanid containing internal pyritic inclusions. Images taken at a magnification of 10x, average diameter of all cysts, 125 µm.

FIGURE 5 in Devonian smooth-walled tasmanids and new insights of life-cycle descriptions through fluorescence microscopy

FIGURE 5. Fluorescence microscopy images of select silica-rich microspherules from the Oatka Creek Formation, Leroy, New York. 5a: tasmanid interpreted to be a gamete sack; 5b" tasmanid interpreted to be a diving stage cyst.

FIGURE 1 in Devonian smooth-walled tasmanids and new insights of life-cycle descriptions through fluorescence microscopy

FIGURE 1. Large scale map of New York state denoting the location of the study area within the region; detail inset of the study location of sampling in Oatka Creek in the city of Leroy, New York; generalized stratigraphic section of Eifellian to Givetian formations of Leroy, New York found within Oatka Creek.

FIGURE 4 in Devonian smooth-walled tasmanids and new insights of life-cycle descriptions through fluorescence microscopy

FIGURE 4. Fluorescence microscopy images of select silica-rich microspherules from the Oatka Creek Formation, Leroy, New York. Black and white arrows denote locations of diminutive spherules within endocysts. Yellow arrows denote the edge of the external wall. Average diameter of tasmanid 4a–c is 125 µm; 4d diameter is 50 µm; 4e tasmanid diameter is 125 µm; 4f tasmanid horizontal diameter is 120 µm with a height of ~130 µm.

opencc-by-4.0May 2024View details →

Data for 'Noninvasive megapixel fluorescence microscopy through scattering layers by a virtual reflection-matrix'

This repository hosts the datasets used in the study 'Noninvasive megapixel fluorescence microscopy through scattering layers by a virtual reflection-matrix.' It includes sets of images of fluorescent samples positioned behind a scattering layer, captured using random illuminations in a microscope setup detailed in the paper. The data correspond to the examples and figures presented in the publication.

opencc-by-4.0Nov 2021View details →

Simultaneous NAD(P)H and FAD fluorescence lifetime microscopy of long UVA–induced metabolic stress in reconstructed human skin

Solar ultraviolet longwave UVA1 exposure of human skin has short-term consequences at cellular and molecular level, leading at long-term to photoaging. Following exposure, reactive oxygen species (ROS) are generated, inducing oxidative stress that might impair cellular metabolic activity. However, the dynamic of UVA1 impact on cellular metabolism remains unknown because of lacking adequate live imaging techniques. Here we assess the UVA1-induced metabolic stress response in reconstructed human skin with multicolor two-photon fluorescence lifetime microscopy (FLIM). Simultaneous imaging of nicotinamide adenine dinucleotide (NAD(P)H) and flavin adenine dinucleotide (FAD) by wavelength mixing allows quantifying cellular metabolism in function of NAD(P)+/NAD(P)H and FAD/FADH2 redox ratios. After UVA1 exposure, we observe an increase of fraction of bound NAD(P)H and decrease of fraction of bound FAD indicating a metabolic switch from glycolysis to oxidative phosphorylation or oxidative stress possibly correlated to ROS generation. NAD(P)H and FAD biomarkers have unique temporal dynamic and sensitivity to skin cell types and UVA1 dose. While the FAD biomarker is UVA1 dose-dependent in keratinocytes, the NAD(P)H biomarker shows no dose dependence in keratinocytes, but is directly affected after exposure in fibroblasts, thus reflecting different skin cells sensitivities to oxidative stress. Finally, we show that a sunscreen including a UVA1 filter prevents UVA1 metabolic stress response from occurring.