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16 results for “quantitative microscopy”
Quantitative phase microscopy timelapse dataset of PNT1A, DU-145 and LNCaP cells with annotated caspase 3,7-dependent and independent cell death
<p>Time-lapse dataset of prostatic cell lines (DU-145, PNT1A, LNCaP) exposed to cell death-inducing compounds (staurosporine, doxorubicin) and black phosphorus. The time-lapse dataset is annotated as follows: (1) cell masks and cell numbers, (2) by cell death type and timepoint of death in the attached xlsx file. This dataset is supplementary to the article:</p> <p>Vicar, T., Raudenska, M., Gumulec, J. <em>et al.</em> The Quantitative-Phase Dynamics of Apoptosis and Lytic Cell Death. <em>Sci Rep</em> <strong>10, </strong>1566 (2020). <a href="https://doi.org/10.1038/s41598-020-58474-w">https://doi.org/10.1038/s41598-020-58474-w</a></p> <p>Correlative fluorescence microscopy is in a separate dataset <a href="https://doi.org/10.5281/zenodo.4531900">10.5281/zenodo.4531900</a></p> <p>Code is available at <a href="https://github.com/tomasvicar/CellDeathDetect">https://github.com/tomasvicar/CellDeathDetect</a></p> <p><strong>Methods</strong></p> <p><em>Cell culture and cultured cell conditions</em><br> LNCaP cell line was established from a lymph node metastase of the hormone-refractory patient and contains a mutation in the AR gene. This mutation creates a promiscuous AR that can bind to different types of steroids. LNCaP cells are AR-positive, PSA-positive, PTEN-negative and harbor wild-type p53 {Skjoth, 2006 #150; Mitchell, 2000 #149}. PNT1A is immortalized non-tumorigenic epithelial cell line. PNT1A cells harbour wild-type p53. However, SV40 induced T-antigen expression inhibits the activity of p53. This cell line had lost the expression of androgen receptor (AR) and prostate-specific antigen (PSA) (Raudenska, 2019). DU-145 cell line is derived from the metastatic site in the brain and contains P223L and V274F mutations in p53. This cell line is PSA and AR-negative and androgen independent (Chappell, 2012). All cell lines used in this study were purchased from HPA Culture Collections (Salisbury, UK). and were cultured in RPMI-1640 medium with 10 % FBS. The medium was supplemented with antibiotics (penicillin 100 U/ml and streptomycin 0.1 mg/ml). Cells were maintained at 37°C in a humidified (60%) incubator with 5% CO2 (Sanyo, Japan).</p> <p><em>Correlative time-lapse quantitative phase-fluorescence imaging</em></p> <p>QPI and fluorescence imaging were performed by using multimodal holographic microscope Q-PHASE (TESCAN, Brno, Czech Republic). To determine the amount of caspase-3/7 product accumulation, cells were loaded with 2 µM CellEventTM Caspase-3/7 Green Detection Reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s protocol and visualized using FITC 488 nm filter. To detect the cells with a loss of plasma membrane integrity, cells were stained with 1 ug/ml propidium iodide (Sigma Aldrich Co., St. Louis, MO, USA) and visualized using TRITC 542 nm filter. Nuclear morphology and chromatin condensation were analyzed using Hoechst 33342 nuclear staining (ENZO, Lausen, Switzerland) and visualized using DAPI 461 nm filter. Cells were cultivated in Flow chambers μ-Slide I Lauer Family (Ibidi, Martinsried, Germany). To maintain standard cultivation conditions (37°C, humidified air (60%) with 5% CO2) during time-lapse experiments, cells were placed in the gas chamber H201 - for Mad City Labs Z100/Z500 piezo Z-stages (Okolab, Ottaviano NA, Italy). To image enough cells in one field of view, lens Nikon Plan 10/0.30 were chosen. For each cell line and each treatment, seven fields of view were observed with the frame rate 3 mins/frame for 24 or 48 h respectively. Holograms were captured by CCD camera (XIMEA MR4021 MC-VELETA), fluorescence images were captured using ANDOR Zyla 5.5 sCMOS camera. Complete quantitative phase image reconstruction and image processing were performed in Q-PHASE control software. Cell dry mass values were derived according to {Prescher, 2005 #177} and {Park, 2018 #178} from the phase (eq. (1)), where m is cell dry mass density (in pg/μm2), φ is detected phase (in rad), λ is wavelength in μm (0.65 μm in Q-PHASE), and α is specific refraction increment (≈0.18 μm3/pg). All values in the formula except the Phi are constant. Phi (Phase) is the value measured directly by the microscope. Integrated phase shift through a cell is proportional to its dry mass, which enables studying changes in cell mass distribution (Park et al., 2018).</p> <p><strong>File description</strong></p> <p>There are three archives included for particular cell lines:</p> <ul> <li>QPI_annotated_timelapse_DU145.zip for DU-145 cells</li> <li>QPI_annotated_timelapse_PNT1A.zip for PNT1A cells</li> <li>QPI_annotated_timelapse_LNCaP.zip for LNCaP cells</li> </ul> <p>The archive includes of following files:</p> <ul> <li><strong>Tiff with time-lapse</strong> quantitative phase image (32-bit files 600x600px with values in pg/um2 with framerate 1 frame/3minutes with 1.59 px/um), named <em>QPI_cellline_treatment_FOV.tiff</em></li> <li><strong>Tiff file with segmentation</strong> mask for particular cells named <em>mask_cellline_treatment_FOV.tiff</em></li> <li><strong>xlsx table</strong> with cell death type (1 for apoptosis, 2 for necrosis, 3 for ambiguous/surviving) and time of death for representative cell number from mask, named <em>labels_cellline_treatment_FOV.xlsx</em></li> </ul> <p>file naming has following conventions:</p> <ul> <li>cell names: DU145, PNT1A, LNCaP for particular cell line</li> <li>treatments: st, bp, do for staurosporine, black phosphorus and doxorubicin</li> <li>fields of view: 1 to 7</li> </ul> <p>e.g. QPI_DU145_st_4.tif, mask_DU145_st_4.tif, labels_DU145_st_4.xlsx</p> <p>Note that correlative fluorescence images are available at <a href="https://doi.org/10.5281/zenodo.4531900">10.5281/zenodo.4531900</a></p>
Figure 5. - Scanning electron microscopy. A in Resorption of scales in Atlantic salmon (Salmo salar) during its anadromous migration: a quantitative study
Figure 5. - Scanning electron microscopy. A: View of a spawning male scale (F = focus); B: Detail of the anterior field of the same scale showing some Howship's lacunae (arrows), which are evidence for osteoclastic resorption.
Dominance of Auger excitation in beam heating in transmission electron microscopy: Irradiation experiments and quantitative thermal analysis of α-Al2O3
<p>The collection of uploaded files constitutes a dataset supporting our findings, titled Dominance of Auger excitation in beam heating in transmission electron microscopy: Irradiation experiments and quantitative thermal analysis of α-Al<sub>2</sub>O<sub>3</sub>, to be submitted to a scientific journal.</p> <p>The co-authors are Jihye Kwon and Hyoung Seop Kim, both at Pohang University of Science and Technology (POSTECH), Republic of Korea</p>
Dataset for: AI-enabled Lorentz microscopy for quantitative imaging of nanoscale magnetic spin textures
<p>Data used in the publication: AI-enabled Lorentz microscopy for quantitative imaging of nanoscale magnetic spin textures</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>
Data from "Quantitative determination of atomic buckling of silicene by atomic force microscopy"
<p>Data From the publication "Quantitative determination of atomic buckling of silicene by atomic force microscopy"</p>
Annotated quantitative phase microscopy cell dataset of various adherent cell lines for segmentation purposes
<p>This dataset contains microscopic images of multiple cell lines captured by quantitative phase microscopy (QPI) without use of any fluorescent labeling and a manually annotated ground truth for subsequent use in segmentation algorithms. Dataset also includes images reconstructed according to the methods described below in order to ease further segmentation. </p> <p>Our data consist of quantitative phase microscopy images:</p> <ul> <li>244 labelled images of PC-3 (7,907 cells), 205 labelled PNT1A (9,288 cells), 25 labelled images of G361, 25 labelled images of A2050 and 25 labelled images of HOB cells , in the paper designated as "<em>labelled"</em>, and</li> <li>1,819 unlabelled images with a mixture of 22Rv1, A2058, A2780, DU145, Fadu, G361, HOB and LNCaP used for pretraining, in the paper designated as "<em>unlabelled"</em>.</li> </ul> <ul> <li>See Vicar et al. XXXX 2021 DOI XXX (TBA after publishing)</li> <li>Code using this dataset is available at <a href="https://github.com/tomasvicar/Deep-QPI-Cell-Segmentation">github.com/tomasvicar/Deep-QPI-Cell-Segmentation</a></li> </ul> <p><strong>Materials and methods </strong></p> <p>A set of adherent cell lines of various origins, tumorigenic potential, and morphology were used in this paper (PC-3, PNT1A, 22Rv1, DU145, LNCaP, A2058, A2780, Fadu, G361, HOB). PC-3, PNT1A, 22Rv1, DU145, LNCaP, A2780, and G361 cell lines were cultured in RPMI-1640 medium, A2058, FaDu, and HOB cell lines were cultured in DMEM-F12 medium, all supplemented with antibiotics (penicillin 100 U/ml and streptomycin 0.1 mg/ml), and with 10% fetal bovine serum (FBS). Prior to microscopy acquisition, the cells were maintained at 37 °C in a humidified (60%) incubator with 5% CO\textsubscript{2} (Sanyo, Japan). For acquisition purposes, the cells were cultivated in the Flow chamber µ-Slide I Luer Family (Ibidi, Martinsried, Germany). To maintain standard cultivation conditions during time-lapse experiments, cells were placed in the gas chamber H201 - for Mad City Labs Z100/Z500 piezo Z-stage (Okolab, Ottaviano NA, Italy). For the acquisition of QPI, a coherence-controlled holographic microscope (Telight, Q-Phase) was used. Objective Nikon Plan 10×/0.3 was used for hologram acquisition with a CCD camera (XIMEA MR4021MC). Holographic data were numerically reconstructed with the Fourier transform method (described in Slaby, 2013 and phase unwrapping was used on the phase image. QPI datasets used in this paper were acquired during various experimental setups and treatments. In most cases, experiments were conducted with the time-lapse acquisition. The final dataset contains images acquired at least three hours apart.</p> <p><strong>Folder structure and file and filename description</strong></p> <p><strong>labelled </strong><em>(labelled)</em>: cells with segmentation labels, e.g.<br> 00001_PC3_img.tif - 32bit tiff image (in pg/um2 values)<br> 00001_PC3_mask.png - 8bit image with mask with unique grayscale value corresponding to single cell in FOV.</p> <p><strong>unlabelled </strong><em>(unlabelled)</em>: 11 varying cell lines, total 1819 FOVs, 32bit tiff image (in pg/um2 values)</p> <p> </p>
3D-Imaging and Quantitative Subsurface Dielectric Constant Measurement Using Peak Force Kelvin Probe Force Microscopy
<p>We demonstrate a new approach to simultaneously measure the dielectric constants of buried structures and interfaces by combining peak force tapping quantitative Nano-mechanical mapping (PF QNM) and frequency-modulated Kelvin probe force microscopy (FM-KPFM). The developed method paves the way for 3D-imaging of dielectric constants of composite materials and heterostructures.</p>
Data for: EMBER multi-dimensional spectral microscopy enables quantitative determination of disease- and cell-specific amyloid strains
Open the record for dataset details and reuse information.
Representative data accompanying the manuscript: Four-dimensional quantitative analysis of cell plate development in Arabidopsis using lattice light sheet microscopy identifies robust transition points between growth phases
<p>Representative data accompanying the manuscript: Sinclair R, Wang M, Jawaid MZ, Longkumer T, Aaron J, Rossetti B, Wait E, McDonald K, Cox D, Heddleston J, Wilkop T, Drakakaki G. (2024). <em>Four-dimensional quantitative analysis of cell plate development in Arabidopsis using lattice light sheet microscopy identifies robust transition points between growth phases.</em> J Exp Bot. 2024 Mar 4: erae091. doi: 10.1093/jxb/erae091.</p> <p>The data show YFP–RABA2a dynamics in dividing cells of Arabidopsis root tips using lattice light sheet microscopy. Treatments with or without Endosidin 7, a cytokinesis-specific callose deposition inhibitor, are shown.</p> <p>Data: </p> <p>22.3 YFP-RABA2A. </p> <p>23.9 YFP-RABA2A ES7 </p>
Quantitative measures of corneal transparency, derived from objective analysis of depth-resolved corneal images, demonstrated with full-field optical coherence tomographic microscopy
<p>Supporting data for: <a href="https://zenodo.org/record/2579947">Quantitative measures of corneal transparency, derived from objective analysis of depth-resolved corneal images, demonstrated with full-field optical coherence tomographic microscopy</a></p>
Raw and processed data for publication "Quantitative microscopy reveals dynamics and fate of clustered IRE1alpha"
<p>This dataset contains all raw and processed data for our PNAS paper titled "Quantitative microscopy reveals dynamics and fate of clustered IRE1alpha". Using the associated analysis code (10.5281/zenodo.3544482), all figures in the paper can be reproduced from the data in this upload.</p> <p>Abstract of the paper is included below:</p> <p>"The endoplasmic reticulum (ER) membrane-resident stress sensor IRE1 governs the most evolutionarily conserved branch of the unfolded protein response. Upon sensing an accumulation of unfolded proteins in the ER lumen, IRE1 activates its cytoplasmic kinase and ribonuclease (RNase) domains to transduce the signal. IRE1 activity correlates with its assembly into large clusters, yet the biophysical characteristics of IRE1 clusters remain poorly characterized. We combined super-resolution microscopy, single-particle tracking, fluorescence recovery and photoconversion to examine IRE1 clustering quantitatively in living human and mouse cells. Our results revealed that (1) by contrast to qualitative impressions gleaned from microscopic images, IRE1 clusters comprise only a small fraction (~5%) of the total IRE1 in the cell. (2) IRE1 clusters have complex topologies that display features of higher-order organization. (3) IRE1 clusters contain a diffusionally constrained core, indicating that they are not phase-separated liquid condensates. (4) IRE1 molecules in clusters remain diffusionally accessible to the free pool of IRE1 molecules in the general ER network. (5) When IRE1 clusters disappear at later timepoints of ER stress as IRE1 signaling attenuates, their constituent molecules are released back into the ER network and not degraded. (6) IRE1 cluster assembly and disassembly are mechanistically distinct. (7) IRE1 clusters’ mobility is nearly independent of cluster size. Taken together, these insights define the clusters as dynamic assemblies with unique properties. The analysis tools developed for this study will be widely applicable to investigations of clustering behaviors in other signaling proteins."</p>
Data related to "Quantitative phase microscopies:accuracy comparison"
<p>This repository contains the data related to this article:</p> <p><em>Quantitative phase microscopies: accuracy comparison</em><br>P. C. Chaumet, P. Bon, G. Maire, A. Sentenac, G. Baffou<br><strong>arXiv</strong>, 2403.11930 (2024)</p> <p>It was created the 27th of March, before the article was accepted for publication.</p> <ul> <li>Folder theo</li> <li>Folder 230719 contains the data of Fig. 6 (*nonoise* folder) and Fig. 7 (*noisy* folder), and also of Fig. 12, in the noisy/DPC and nonoise/DPC folders.</li> <li>Folder 230728_CGMdistance contains data of Fig. 9</li> <li>Folder 230728_DPMdiameter contains data of Fig. 11a,b</li> <li>Folder 230728_DPMdiameter_NA contains data of Fig. 11c,d</li> <li>Folder 230728_FPMdiameter contains data of Fig. 13a,</li> <li>Folder 230728_FPMdiameter_NA contains data of Fig. 13c,d</li> <li>Folder 230728_TIEzShift_NP contains data of Fig. 14a,c.</li> <li>Folder 230728_TIEzShift_cell contains data of Fig. 14b,d.</li> </ul> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Experimentally analysed data for Quantitative Microbiology with Microscopy: Effects of Projection and Diffraction
<p>Experimentally analysed data for Quantitative Microbiology with Microscopy: Effects of Projection and Diffraction</p> <p> </p>
Dataset for paper "Dominance of Auger excitation in beam heating in transmission electron microscopy: Irradiation experiments and quantitative thermal analysis of α-Al2O3"
<p>The collection of uploaded files constitutes a dataset supporting our findings, titled Dominance of Auger excitation in beam heating in transmission electron microscopy: Irradiation experiments and quantitative thermal analysis of α-Al<sub>2</sub>O<sub>3</sub>, to be submitted to a scientific journal. The input file for finite element analysis, with the ".inp" extension, is also included.</p>
Recopliación de datos cuantitativos extraídos del análisis textural de la colección de referencia experimental sobre tratamiento de superficie en cerámica a mano mediante microscopía óptica confocal / Compilation of quantitative data extracted from the textural analysis of the experimental reference collection on surface treatment of handmade pottery by confocal optical microscopy.
<p>This repository contains the quantitative data and stadistical test extracted from the textural analysis of the experimental reference collection on surface treatment of handmade pottery by confocal optical microscopy.</p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.