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4 results for “Single-cell microscopy”
Data for: "A high-throughput microscopy method for single-cell analysis of event-time correlations in nanoparticle-induced cell death"
<p>Data related to the publication Murschhauser <em>et al.</em>: <a href="https://doi.org/10.1038/s42003-019-0282-0">A high-throughput microscopy method for single-cell analysis of event-time correlations in nanoparticle-induced cell death</a>. It contains fluorescence time traces of single cells marked with cell-event markers and observed by time-lapse microscopy. The cells were treated with nanoparticles at different doses (NP25 and NP100), with staurosporine (sts) or were left untreated for control (ctrl). See the above-mentioned publication for more details.</p> <p>The format of the data is described below.</p> <p>The file <code>Data_A549.zip</code> contains data measured with A549 cells, and the file <code>Data_Huh7.zip</code> contains data measured with Huh7 cells. Both files have the same structure. Each file contains the directories <code>Raw</code> and <code>Fitted</code> as well as a checksum file. The <code>Raw</code> directory contains single-cell fluorescence time courses as obtained by time-lapse microscopy. The <code>Fitted</code> directory contains the results of fitting model functions as well as properties of identified events, such as event times. The checksum file contains SHA256 checksums of all files within these directories and can be used to check file integrity.</p> <p>Both directories contain measurement directories. Each measurement directory contains the data corresponding to one experiment. The name of the measurement directory is the measurement identifier. Each measurement directory contains condition directories. Each condition directory contains data corresponding to one condition measured in the measurement and is named after the condition. Each condition directory contains marker directories. They are named after the fluorescence markers measured and contain files with single-cell data corresponding to the respective markers.</p> <p>The names of those files consist of multiple parts separated by underscores. The first two parts identify a position of the microscope. Since pairs of markers were measured, each position is present in two marker directories. The third part is the measurement identifier. The other parts will be described below.</p> <p>The <code>Raw</code> directory contains only CSV files with the raw fluorescence time courses. The filenames contain no other parts and have the suffix “.txt”. The first row of each CSV file is the time (in units of 10 minutes), and the other rows are the fluorescence time courses of the cells observed at the corresponding position (in arbitrary units). Each file in the <code>Raw</code> directory corresponds to a group of files in the <code>Fitted</code> directory.</p> <p>The <code>Fitted</code> directory contains three types of CSV files. Their names have “ALL” as fourth part, a session identifier as sixth part and the suffix “.csv”. The fifth part indicates the type of file and is one of the following:</p> <ul> <li>“PARAMS” indicates the estimated values for the model parameters. Each row stands for one cell and each column for a parameter of the model function fitted to the data. The model functions are published with the <a href="https://doi.org/10.5281/zenodo.1418465">fitting software</a>.</li> <li>“SIMULATED” indicates the fitted traces. The traces are calculated using the model functions and the estimated parameters. The format is the same as for the raw traces, but the time is in units of hours and has a higher resolution.</li> <li>“STATE” indicates additional information extracted from the fitted traces. Each row stands for a cell and each column for a property. The first column is the number of the cell. The second column is the event time found (in hours); non-finite values indicate that no event time was found. The third and fourth columns contain the absolute and relative amplitude of the trace, respectively. The fifth column is the logarithmic likelihood of the best fit. The sixth column indicates an algorithm used for postprocessing, and the seventh column indicates the trace slope at the event. See the fitting software for details.</li> </ul> <p> </p>
Microscopy data for the paper: Analysis and design of single-cell experiments to harvest fluctuation information while rejecting measurement noise.
<p>Microscopy data for the paper: Analysis and design of single-cell experiments to harvest fluctuation information while rejecting measurement noise.</p> <p> </p> <p>List of files used for each dataset.</p> <p> </p> <p>Dataset 0 : MS2-CY5_Cyto543_560_woStim</p> <p> Images in the dataset :</p> <p> ROI001_XY1657814108_Z00_T0_merged.tif - Image Id Number: 0</p> <p> ROI002_XY1657815441_Z00_T0_merged.tif - Image Id Number: 1</p> <p> ROI003_XY1657814110_Z00_T0_merged.tif - Image Id Number: 2</p> <p> ROI004_XY1657814111_Z00_T0_merged.tif - Image Id Number: 3</p> <p> ROI005_XY1657814112_Z00_T0_merged.tif - Image Id Number: 4</p> <p> ROI006_XY1657814113_Z00_T0_merged.tif - Image Id Number: 5</p> <p> ROI007_XY1657814114_Z00_T0_merged.tif - Image Id Number: 6</p> <p> ROI008_XY1657814115_Z00_T0_merged.tif - Image Id Number: 7</p> <p> ROI009_XY1657814116_Z00_T0_merged.tif - Image Id Number: 8</p> <p> ROI010_XY1657814117_Z00_T0_merged.tif - Image Id Number: 9</p> <p> ROI011_XY1657814118_Z00_T0_merged.tif - Image Id Number: 10</p> <p> ROI012_XY1657814119_Z00_T0_merged.tif - Image Id Number: 11</p> <p> </p> <p>Datset 1 : MS2-CY5_Cyto543_560_18minTPL_5uM</p> <p> Images in the dataset :</p> <p> ROI001 - Position 1_XY1657818948_Z00_T0_merged.tif - Image Id Number: 0</p> <p> ROI001 - Position 2_XY1657818949_Z00_T0_merged.tif - Image Id Number: 1</p> <p> ROI001 - Position 4_XY1657818951_Z00_T0_merged.tif - Image Id Number: 2</p> <p> ROI001 - Position 5_XY1657818952_Z00_T0_merged.tif - Image Id Number: 3</p> <p> ROI001 - Position 6_XY1657818953_Z00_T0_merged.tif - Image Id Number: 4</p> <p> ROI001 - Position 7_XY1657818954_Z00_T0_merged.tif - Image Id Number: 5</p> <p> ROI001 - Position 8_XY1657818955_Z00_T0_merged.tif - Image Id Number: 6</p> <p> ROI001 - Position 9_XY1657818956_Z00_T0_merged.tif - Image Id Number: 7</p> <p> ROI001 - Position 10_XY1657818957_Z00_T0_merged.tif - Image Id Number: 8</p> <p> ROI001 - Position 11_XY1657818958_Z00_T0_merged.tif - Image Id Number: 9</p> <p> ROI001 - Position 12_XY1657818959_Z00_T0_merged.tif - Image Id Number: 10</p> <p> </p> <p>Dataset 2: MS2-CY5_Cyto543_560_5hTPL_5uM</p> <p> Images in the datset :</p> <p> ROI001_XY1657822809_Z00_T0_merged.tif - Image Id Number: 0</p> <p> ROI002_XY1657822933_Z00_T0_merged.tif - Image Id Number: 1</p> <p> ROI003_XY1657822934_Z00_T0_merged.tif - Image Id Number: 2</p> <p> ROI005_XY1657822936_Z00_T0_merged.tif - Image Id Number: 3</p> <p> ROI006_XY1657822937_Z00_T0_merged.tif - Image Id Number: 4</p> <p> ROI007_XY1657822938_Z00_T0_merged.tif - Image Id Number: 5</p> <p> ROI008_XY1657822939_Z00_T0_merged.tif - Image Id Number: 6</p> <p> ROI010_XY1657822941_Z00_T0_merged.tif - Image Id Number: 7</p> <p> ROI013_XY1657822944_Z00_T0_merged.tif - Image Id Number: 8</p> <p> ROI014_XY1657822945_Z00_T0_merged.tif - Image Id Number: 9</p> <p> ROI015_XY1657822946_Z00_T0_merged.tif - Image Id Number: 10</p> <p> ROI016_XY1657822947_Z00_T0_merged.tif - Image Id Number: 11</p> <p> ROI017_XY1657822948_Z00_T0_merged.tif - Image Id Number: 12</p> <p> ROI018_XY1657822949_Z00_T0_merged.tif - Image Id Number: 13</p> <p> </p> <p> </p>
Berkeley Single-Cell Computational Microscopy (BSCCM) dataset
Open the record for dataset details and reuse information.
Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy
GEO Series GSE160784. Homo sapiens. 3 samples. Type: Other.
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