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146 results for “Phase Imaging”
Noise Resistant Phase Imaging with Intensity Correlation
<p>Raw data for the arXiv:2301.11969 "Noise Resistant Phase Imaging with Intensity Correlation"</p> <p>Supported by the National Science Centre, Poland, grant number 2022/45/N/ST2/04249</p>
Multi-colour super-resolution images of untreated and rifampicin-treated Xenorhabdus doucetiae (LB, exponential phase)
<p> This dataset and CARE model is part of the publication "<strong>Transertion and cell geometry organize the </strong><i><strong>Escherichia coli</strong></i><strong> nucleoid during rapid growth</strong>".</p><p>It contains all SMLM images that were used for the publication, as well as the single-cell regions of interest for analyses.</p><p>Xenorhabdus doucetiae chromosomally expressing MreBsw-sfGFP were grown to exponential phase in LB Lennox and antibiotics were added for 0-30 min. Cultures were then chemically fixed, permeabilised and imaged for the nucleoid (JF646-Hoechst) and membranes (Nile Red) using PAINT.</p><p>More information can be found in the publication.</p>
Dataset of PNT1A and PC-3 cells - efect of FITC phototoxicity, quantitative phase imaging (1/2)
<p>Part of article Feith, M,Vičar, T., Gumulec, J., Raudenská, M. Wingren, AG, Masařík, M., Balvan, J. Quantitative Phase Dynamics of Cancer Cell Populations Affected by Blue Light, <em>Appl. Sci.</em> <strong>2020</strong>, <em>10</em></p> <p>Increased exposition to blue light may induce many changes in cell behavior and significantly affect the critical characteristics of cells. Here we show that multimodal holographic microscopy (MHM) within advanced image analysis is capable of correctly distinguishing between changes in cell motility, cell dry mass, cell density, and cell death induced by blue light. We focused on the effect of blue light with a wavelength of 485 nm on morphological and dynamical parameters of four cell lines, malignant PC-3, A2780, G361 cell lines, and the benign PNT1A cell line. We used MHM with blue light doses 24 mJ/cm<sup>2</sup>, 208 mJ/cm<sup>2 </sup>and two kinds of expositions (500 and 1000 ms) to acquire real-time quantitative phase information about cellular parameters. It has been shown that specific doses of the blue light significantly influence cell motility, cell dry mass and cell density. These changes were often specific for the malignant status of tested cells. Blue light dose 208 mJ/cm<sup>2 </sup>× 1000 ms affected malignant cell motility but did not change the motility of benign cell line PNT1A. This light dose also significantly decreased proliferation activity in all tested cell lines but was not so deleterious for benign cell line PNT1A as for malignant cells. Light dose 208 mJ/cm<sup>2 </sup>× 1000 ms oppositely affected cell mass in A2780 and PC-3 cells and induced different types of cell death in A2780 and G361 cell lines. Cells obtained the least damage on lower doses of light with shorter time of exposition.</p> <p><strong>Materials and Methods </strong></p> <p><em>Cell Lines</em></p> <p>The PC-3, A2780, PNT1A, and G361 cell lines were purchased from HPA Culture Collections (Salisbury, UK). PC-3 prostate cancer cell line was derived from bone metastasis of a 4-grade prostatic adenocarcinoma of a 62-year-old Caucasian male The A2780 cell line was derived from the ovarian carcinoma of a nontreated patient according to ECACC. PNT1A cell line was established from prostatic epithelial tissue of healthy 35-years old male and immortalized by plasmid transfection containing the SV40 genome with defective replication origin. The G361 cell line was established from a malignant melanoma of a 31-year-old male Caucasian. The G361 cells produce melanin for up to 50 population doublings. As the aim of this study is to compare the effect of blue light on the cell lines differing by morphology, transformation state, sensitivity to cell death, and origin, we decided to use the cell lines listed above. PC-3 cells are larger in comparison with small A2780 cells. Benign PNT1A cell line differs from malignant PC-3, and all four cell lines are derived from diverse tissues of origin. Furthermore, melanoma G361 cells expressing melanin may differ in the reaction of cells to blue light exposure.</p> <p></p> <p><em>Cell Cultivation</em></p> <p>All four cell lines were cultivated in 25 cm<sup>2</sup> flasks with 5 ml of media at 37 °C in a humidified incubator (60%) with 5% CO<sub>2 </sub>(Sanyo, Osaka City, Japan). Cell lines A2780, PNT1A and G361 were cultured in RPMI-1640 medium with phenol red indicator, L–glutamine, FBS and antibiotics penicillin/streptomycin (Sigma Aldrich Co., St. Louise, MO, USA). For the PC-3 cell line cultivation, Ham´s F-12 medium with FBS and antibiotics (Sigma Aldrich Co., St. Louis, MO, USA) was used. The same supplementation with antibiotics (penicillin 100 U/mL and streptomycin 0.1 mg/mL) and 10% FBS was used in both media. The cell medium was changed two times per week. Cell subculturing was done with 10% of trypsin solution (PAA, Pasching, Austria) with previous washing with EDTA (0.02% in PBS buffer).</p> <p><em>QPI and Holographic Microscopy and Fluorescence Setting</em></p> <p>QPI was performed by using a Q-PHASE multimodal holographic microscope (Telight, Brno, CZ). The Q-PHASE is equipped with fluorescence module using a halogen lamp as a non-coherent source of blue light. In this work, the module was used as a source of blue light for treatment of observed cell lines. The 485 nm light waves are emitted by the fluorescence light source of the attached module. Before the imaging experiment, cells were cultivated overnight in a concentration of 7000 cells/mL in flow chamber µ-Slide I Lauer Family (Ibidi, Martinsried, Germany). During the measurements, the chamber with cells was incubated in 37 °C humidified, 5% CO<sub>2</sub> atmosphere in H201–for Mad City Labs Z100/Z500 piezo Z-stages (Okolab, Ottaviano NA, Italy). Images and holograms were captured with lens Nikon Plan 10/0.3 and CCD camera (XIMEA MR4021 MC-VELETA, Münster, Germany) respectively. The fluorescence mode used was a plasma light source (Sutter Instrument Lambda XL Novato, CA, USA). Cells were irradiated with a 485 nm light with a 25 nm bandwidth. Light doses 0 mJ/cm<sup>2</sup>, 24 mJ/cm<sup>2</sup> and 208 mJ/cm<sup>2 </sup>were achieved by the combination of time exposition and light intensity.</p> <p>The images were acquired automatically from seven positions every 3 min for 24 h. Holographic images were collected by custom software and raw data were numerically reconstructed. The numerical reconstruction was performed by custom software where the established methods of the fast Fourier-transform and phase unwrapping are implemented. The output from the software is an unwrapped phase image. This image has high intrinsic contrast and can be processed by an available image processing software. The unwrapped phase image is integrated phase shift through the cell and it is proportional to integrated cell dry mass density.</p> <p></p>
Image analysis data for the study of the reactivity of the phases in Nd-Fe-B magnets etched with HCl-saturated Cyphos IL 101
<p>Scanning electronic microscopy (SEM), Energy dispersive X-rays Spectroscopy (EDS) and image analysis have been used as techniques to analyse the results of etching experiments carried on NdFeB permanent magnets by using the ionic liquid Cyphos IL 101 saturated with HCl. Image analysis is for the first time reported in the literature as a technique for corrosion studies.</p> <p>Operational conditions of the analysis equipment were the following:</p> <p>- The samples were analyzed via electron microscopy and image analysis. Scanning electron microscope (SEM) pictures and energy dispersed spectra (EDS) were collected with a JEOL JSM 5800 microscope, operating at 20 kV. The polished samples were made conductive by spraying a carbon layer on them using a Balzer SCD 050 sputter coater.</p> <p>- The EDS analysis were collected as average on 5 points per each SEM picture</p> <p>- A commercial software, ImageJ®, was used for the image analysis. Two data were analysed: the Feret diameter, d<sub>F</sub>, and the percentage of etched area, %area. The SEM images were converted to 8-bit grayscale, from 0 to 255 number of grey ranges. Simple linear scaling was applied</p>
Electrostatic OAM generator with boundary condition - Phase images of the boundary conditions
<p>Here reported is the dataset that can be used to reconstruct the phase of the electron beam (process already done for the files which have a C_P in the name) after it has interacted with the electrodes that are used as boundary condition for our electrostatic variable electron vortex beam generator that allow to improve its functioning.</p> <p> </p>
Phase contrast images of Hierodula membranacea spermatocytes in metaphase I
<p>These are phase contrast images of <em>Hierodula membranacea</em> primary spermatocytes. For each image, 608 px=10 µm.</p>
GOIMAI DataSet-Phase-I of high-resolution macroscopic images for the identification of wood species
<p>GOIMAI Phase I is a wood species dataset obtained through magnifying lenses. The inputs needed in our laboratory were a mid-range mobile phone (e.g. Samsung Galaxy S7), a magnifying lens with a universal clamp attached to the lens of the mobile phone (in our case with 24x magnifier) and the wood sample itself.</p> <p>GO IMAI project - Identificación de madera por dispositivo móvil. <br>Convocatoria EI-Agri Programa Nacional de Desarrollo Rural 2014-2020 por el Ministerio de Agricultura, Pesca y Alimentación y el Fondo Europeo Agrícola de Desarrollo Rural (FEADER).</p>
Reactions of cold argon plasma with condensed-phase peptides and proteins for mass spectrometry imaging and structural elucidation - ESI
<p>ESI data for the paper 'Reactions of cold argon plasma with condensed-phase peptides and proteins for mass spectrometry imaging and structural elucidation'.</p>
Imaging material yielding and phase transitions in shock-compressed matter
<p>Extended data sources for manuscript "Imaging material yielding and phase transitions in shock-compressed matter"</p>
Raw diffraction images of plant vacuolar iron transporter VIT1 (phasing data by Hg-SIR)
<p>Diffraction images of full-length VIT1 for Hg-SIR phasing. All data were collected from loop-harvested crystals on BL32XU, SPring-8 at a wavelength of 1 Å using the EIGER X 9M detector.</p> <p>For Hg-bound VIT1, six helical (71-210°/crystal) datasets were collected. From native (without Hg) crystals, 24 helical (20-90°/crystal) datasets were automatically collected. The crystals belonged to space group <em>C</em>222<sub>1</sub> with unit cell parameter a~47, b~290, c~46 Å.</p> <p>Related entries: <a href="https://zenodo.org/record/2532136">full-length with Co/Zn</a>, <a href="https://zenodo.org/record/2532134">metal binding domain</a><br> </p>
Raw diffraction images of Ferroportin homologue (phasing data by Hg-SIRAS)
<p>Diffraction images of native and mercury-bound Ferroportin homologue from Bdellovibrio bacteriovorus. This phase information was used for PDB entries <a href="http://www.pdb.org/pdb/search/structidSearch.do?structureId=5AYM">5AYM</a> and <a href="http://www.pdb.org/pdb/search/structidSearch.do?structureId=5AYN">5AYN</a>, and indirectly <a href="http://www.pdb.org/pdb/search/structidSearch.do?structureId=5AYO">5AYO</a> (<a href="https://doi.org/10.1038/ncomms9545">Taniguchi et al. 2015</a>). All data were collected from loop-harvested crystals on BL32XU, SPring-8 at a wavelength of 1.00000 Å using the MX225HS CCD detector.</p> <p>From a native crystal, a helical (180°/crystal, 1°/frame) datasets were collected using 12×8 μm<sup>2</sup> beam. From a mercury-derivative crystals, two helical (180°/crystal, 1.5°/frame) datasets were collected using 10×2 μm<sup>2</sup> beam. The crystals belonged to space group <em>P</em>2<sub>1</sub>2<sub>1</sub>2<sub>1</sub> with unit cell parameter a~57, b~86, c~96 Å.</p>
Raw diffraction images of YidC (phasing data by Hg-MAD)
<p>Diffraction images of mercury-bound <em>Bacillus halodurans</em> YidC mutants for Hg-MAD phasing. This phase information was used for PDB entries <a href="http://www.pdb.org/pdb/search/structidSearch.do?structureId=3WO6">3WO6</a> and <a href="http://www.pdb.org/pdb/search/structidSearch.do?structureId=3WO7">3WO7</a> (<a href="https://doi.org/10.1038/nature13167">Kumazaki et al. 2014</a>). All data were collected from loop-harvested crystals on BL32XU, SPring-8 at wavelengths of 1.00000 Å (peak) or 1.00945 Å (edge) using the MX225HE CCD detector.</p> <p>From the M146C mutant, helical (360 or 720°/crystal, 2°/frame) datasets were collected using 10×1 μm<sup>2</sup> beam. From a Y150C mutant, a helical (360°/crystal, 2.5°/frame) dataset was collected using 15×1 μm<sup>2</sup> beam, which was used for phase determination. The crystals belonged to space group <em>P</em>2<sub>1</sub> with unit cell parameter a~44, b~60, c~60 Å, β~100°.</p>
Raw diffraction images of H+/Ca2+ exchanger CAX (phasing data by Hg-MAD)
<p>Diffraction images of mercury-bound H<sup>+</sup>/Ca<sup>2+</sup> exchanger from <em>Archaeoglobus fulgidus</em>. This phase information was used for a PDB entry <a href="https://www.rcsb.org/structure/4KPP">4KPP</a> (<a href="http://science.sciencemag.org/content/341/6142/168">Nishizawa et al. 2013</a>). All data were collected from loop-harvested crystals on BL32XU, SPring-8 at wavelengths of 1.00000 Å (peak), 1.00930 Å (edge), or 1.01300 Å (low remote) using the MX225HE CCD detector.</p> <p>From a mercury-derivatised crystal, helical (360°/crystal, 1°/frame) datasets were collected using 5×1 μm<sup>2</sup> beam. The crystal belonged to space group <em>P</em>2<sub>1</sub> with unit cell parameter a~64, b~98, c~72 Å, β~99°.</p>
Geometric-Phase Microscopy for Quantitative Phase Imaging of Isotropic, Birefringent and SpaceVariant Polarization Samples_experimental dataset
<p>This dataset shares the data presented in the paper "Geometric-Phase Microscopy for Quantitative Phase Imaging of Isotropic, Birefringent and SpaceVariant Polarization Samples" available in open access under http://doi.org/10.1038/s41598-019-40441-9. </p>
Chromocenter image processing and data for "Volume buffering in multi-component phase separation"
<p>Contains image processing code and a csv of the image processing results for the images of chromocenters in mammalian cells for the paper "Volume buffering in multi-component phase separation".</p>
Improving magnetic STEM-differential phase contrast imaging using precession
<p>Scanning transmission electron microscopy datasets and processing files used in the journal publication "<strong>Improving Magnetic STEM-Differential Phase Contrast Imaging using Precession</strong>".</p> <p>DOI link to publication: <a href="https://doi.org/10.1093/micmic/ozad001">https://doi.org/10.1093/micmic/ozad001</a></p> <p> </p> <p><strong>Prerequisites</strong></p> <p>To run the scripts necessary to process the files, the open source packages JupyterLab, HyperSpy, pyXem, and fpd need to be installed. These notebooks were created with these package versions:</p> <ul> <li>hyperspy 1.6.4</li> <li>pyxem 0.13.3</li> <li>fpd 0.2.0</li> <li>jupyterlab 3.2.0</li> </ul> <p> </p> <p><strong>Data files and processing scripts</strong></p> <p>Data files are collected in .zip folders and have names that start with "d00..", while processing scripts are in the Jupyter Notebook .ipynb data format whose names start with "p00..". These files are divided into three main processing steps, outlined as follows:</p> <ol> <li><strong>Processing of raw data</strong>: Raw data files can be found in the d001_scans.zip folder. These are processed with the p002_get_dpc_raw.ipynb script which uses either the center of mass or phase correlation methods.</li> <li><strong>D-scan correction</strong>: The processed files from the previous step are saved in the d002_dpc_raw.zip folder. The p003_get_dpc_cor.ipynb script performs a d-scan correction on these files and saves the output in the d003_dpc_cor.zip folder. <ul> <li><strong>Virtual segmented detector algorithm</strong>: For comparison purposes to the other processing algorithms, a virtual segmented detector algorithm was developed and can be found in the p004_segmented_detector.ipynb script. This algorithm extracts a linear d-scan plane from already processed phase correlation files found in d002_dpc_raw.zip, subtracts it from the raw data files found in d001_scans.zip, and finally performs the processing algorithm.</li> </ul> </li> <li><strong>Plotting files</strong>:<strong> </strong>The p005_plot_dpc_images.ipynb script creates the figures as seen in the journal publication. The input files are those found in d003_dpc_cor.zip from the previous processing step.</li> </ol>
Phase contrast images of bacteria and ground truth segmentations
<p><strong>Name</strong>: Phase contrast images of bacteria </p> <p><strong>Data type</strong>: Paired microscopy images and corresponding labels/masks used for model training, organized as recommended by the <a href="https://imagej.net/plugins/denoiseg">DenoiSeg documentation</a>.</p> <p><strong>Microscopy data type</strong>: Light microscopy (Phase Contrast)</p> <p><strong>Manual annotations</strong>: Labels/masks obtained via manual segmentation. For each region, all cells were annotated manually. Uncertain objects were left unannotated.</p> <p><strong>Microscope</strong>: Zeiss Axio Imager M2 epi-fluorescence microscope with a Zeiss Plan-Apochromat; 100x/1.4 oil DIC objective</p> <p><strong>File format</strong>: .tif (float 32-bits for phase contrast and 16-bit for mask images)</p> <p><strong>Image size</strong>: 256x256 pixels (Pixel size: 64.5 nm)</p> <p> </p> <p>Content: </p> <p>train - raw (33 files) </p> <p> - masks (33 files)</p> <p>test - raw (11 files) </p> <p> - masks (11 files)</p> <p> </p> <p>All images available in the raw folders were normalized by dividing the original images with a gaussian blurred version or the original image (200 pixels). A groovy code working within ImageJ/Fiji corresponding to this operation is as follow:</p> <pre><code class="language-java">ImagePlus normalize(ImagePlus input_image) { flatfield = (new Duplicator()).run(input_image) (new GaussianBlur()).blur(flatfield.getProcessor(), 200) return ImageCalculator.run(input_image, flatfield, "Divide create 32-bit") } import ij.ImagePlus import ij.plugin.Duplicator import ij.plugin.ImageCalculator import ij.plugin.filter.GaussianBlur</code></pre> <p> </p>
Data for Diffusion phase-imaging in anisotropic media using non-linear gradients for diffusion encoding
<p>Diffusion MRI data for experiments on anisotropic synthetic fibre phantom and isotropic agar phantom. </p>
Edge illumination X-ray phase contrast imaging with alternative gratings: dataset
<p>This dataset contains results from Edge illumunation X-ray phase contrast simulations with alternative gratings, as shown in 'Setup.png' The simulations are performed with the monte-carlo software Gate. Postprocessing is done in Matlab. Four different grating geometries were simulated: Conventional, sheared, curved and folded gratings. As phantom, a row of Aluminum cylinders is chosen.</p> <p>The simulation parameters can be found in the excel-file 'Simulation_parameters.xlsx'.</p> <p>The folder 'gate' contains the macros that where used for the monte carlo-simulation.</p> <p>The folder 'matlab' contains the results of post-processing in matlab for each grating geometry. They can be opened with the file 'results_script.m</p> <p>The folder 'results' contains images of the results for each geometry, including, flatfield, projection, threefold contrast and fitting parameters.</p> <table> <tbody> <tr> <td>This research was supported by EU Interreg Flanders - Netherlands Smart*Light (0386), Fonds wetenschappelijk onderzoek (G090020N, G094320N), and Agentschap Innoveren \& Ondernemen (Vlaio) (HBC.2020.2159). Nathanaël Six and Ben Huyge have a PhD fellowship of the FWO (11D8319N, 1S46122N).</td> </tr> </tbody> </table> <p> </p> <p></p>
Phase II Study of Florbetaben (BAY94-9172) PET Imaging for Detection/Exclusion of Cerebral β-amyloid.
ClinicalTrials.gov study NCT00928304. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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