Find research datasets worth reusing

opencc-by-4.0Jan 2021View details →

Long-term live imaging and multiscale analysis identify heterogeneity and core principles of epithelial organoid morphogenesis - Image data

The dataset contains raw imaging data from the work: "Long-term live imaging and multiscale analysis identify heterogeneity and core principles of epithelial organoid morphogenesis" The dataset is organized as the following: the "FigureX_" or SupplementaryFigure_X" suffix in the filename refers to the figure in the paper in which the raw data is analyzed and/or visualized. The data is "raw", i.e. not processed. However, in many cases, maximum projections of the original 3D image stacks have been uploaded due to size limitations. The total size of the image stacks approaches 0.5TB. To access the full 3D image stacks please contact the corresponding author (Francesco Pampaloni, fpampalo@bio.uni-frankfurt.de). Authors Lotta Hof1*, Till Moreth1*, Michael Koch1, Tim Liebisch2, Marina Kurtz3, Julia Tarnick4, Susanna M. Lissek5, Monique M.A. Verstegen6, Luc J.W. van der Laan6, Meritxell Huch7, Franziska Matthäus2, Ernst H.K. Stelzer1, Francesco Pampaloni1§ 1Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany 2Faculty of Biological Sciences, Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany 3Department of Physics, Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany 4Deanery of Biomedical Science, University of Edinburgh, Edinburgh, United Kingdom 5Experimental Medicine and Therapy Research, University of Regensburg, Regensburg, Germany 6Department of Surgery, Erasmus MC – University Medical Center, Rotterdam, The Netherlands 7The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom. Present address: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany *contributed equally §corresponding author: fpampalo@bio.uni-frankfurt.de Abstract Background Organoids are morphologically heterogeneous three-dimensional cell culture systems and serve as an ideal model for understanding the principles of collective cell behaviour in mammalian organs during development, homeostasis, regeneration and pathogenesis. To investigate the underlying cell organisation principles of organoids, we imaged hundreds of pancreas and cholangio carcinoma organoids in parallel using light sheet and bright field microscopy for up to seven days. Results We quantified organoid behaviour at single-cell (microscale), individual-organoid (mesoscale), and entire-culture (macroscale) levels. At single-cell resolution, we monitored formation, monolayer polarisation and degeneration, and identified diverse behaviours, including lumen expansion and decline (size oscillation), migration, rotation and multi-organoid fusion. Detailed individual organoid quantifications lead to a mechanical 3D agent-based model. A derived scaling law and simulations support the hypotheses that size oscillations depend on organoid properties and cell division dynamics, which is confirmed by bright field microscopy analysis of entire cultures. Conclusion Our multiscale analysis provides a systematic picture of the diversity of cell organisation in organoids by identifying and quantifying the core regulatory principles of organoid morphogenesis.

opencc-by-4.0Sep 2024View details →

Long-term live imaging, cell identification and cell tracking in regenerating crustacean legs

Supplementary data and videos for the manuscript 'Long-term live imaging, cell identification and cell tracking in regenerating crustacean legs', by Çevrim, Laplace-Builhé, Sugawara, Rusciano, Labert, Brocard, Almazán and Averof. The supplementary data include: Supplementary Data 1 (.csv file);  Live imaging of regenerating Parhyale legs: image acquisition settings Table with information on the 22 time lapse recordings presented in Figure 3, including image acquisition settings, temperature and duration of the recordings. Supplementary Data 2 (.zip file);  Live imaging of regenerated Parhyale legs: maximum projections Compressed folder including maximum projections for each of the 22 time lapse recordings presented in Figure 3. These files were generated by projecting all or a subset of the z slices acquired at each time point. A 20 micron scale bar was added on the first time point. These files serve as a quick way to examine the 22 time lapse recordings. Supplementary Data 3 (22 .tif files);  Live imaging of regenerated Parhyale legs: complete datasets Complete image 3D+T hyperstacks for each of the 22 time lapse recordings presented in Figure 3. These files have been generated by concatenating the original image stacks and correcting any image shifts, as described in the Methods section of the paper. Supplementary Data 4 (.zip file);  Analysis of trade-offs of imaging resolution and image quality The data used for the analysis of trade-offs in imaging and the results shown in Table 1 are included in this compressed folder. Folders for the original recording (labelled 00), for each of the subsampled datasets (labelled 01 to 05), and for the denoised and deconvoluted datasets each include the corresponding image data and ground truth cell tracking files (.tif, .h5, .xml and .mastodon files) and three sets of cell track predictions (.mastodon files). There are also separate folders containing the Elephant detection and flow model parameters for each set of predictions. Supplementary Data 4 (.zip file);  Analysis of trade-offs of imaging resolution and image quality The data used for the analysis of trade-offs in imaging and the results shown in Table 1 are included in two folders. The folder named Image_and_tracking_data includes the image data (.tif, .h5, .xml), ground truth cell tracking files (.mastodon files) and three sets of cell track predictions (.mastodon files) for the original recording (labelled 00), for each of the subsampled datasets (labelled 01 to 05), and for the denoised and deconvoluted datasets. It also includes separate folders containing the Elephant detection and flow model parameters for each set of predictions. The folder named CTC_tracking_results includes the ground-truth data along with three sets of predictions for detection and tracking for each dataset, following the Cell Tracking Challenge format. For each dataset we include label image files (.tif) for every time point along with tracking results in .txt format, and each results directory (01_RES_*) also contains the evaluation results from the Cell Tracking Challenge Evaluation Software. For a detailed explanation of the folder structure, please refer to the Cell Tracking Challenge documentation. Supplementary Data 5 (.zip file);  Tracking the progenitors of spineless-expressing cells in the distal carpus The data used to generate Figure 7 are included in this compressed folder, including the live imaging and cell tracking files (.h5, .xml and .mastodon files) and the image stack of the spineless and futsch HCR and DAPI stainings (.tif file). Channel 2 shows spineless expression (mostly nascent transcripts in nuclei), as well as background signal in epidermal nuclei (possibly due to photoconversion of DAPI, see Karg & Golic 2018, Chromosoma 127: 235-245) and strong autofluorescence in granular cells (also visible in channel 1, depicting futsch HCR). Supplementary Data 6 (.txt file);  Sequences of Parhyale genes targeted by the HCR probes The sequences are provided in FASTA format. Supplementary Data 7 (.zip file);  Apoptosis in legs that have not been subjected to live imaging The data used to generate Figure 2 supplement 2 are contained in this compressed folder, including 9 image stacks of T4 and T5 legs fixed and stained with DAPI 3 days post amputation (with apoptotic nuclei marked) and a .txt file containing the apoptotic cell counts. Supplementary Data 8 (.zip file);  Analysis of tracking performance in relation to imaging depth The data used to generate Figure 5 are contained in this compressed folder, including separate folders for the data extracted from the analysis of datasets #1 to #5. Each folder includes data from three replicates (batches 001 to 003), with .csv files listing the z location of nucleus centroids (in µm) for the nuclei that were incorrectly detected by Elephant – either as false positives (FP) or as false negatives (FN) – and the ground truth data (GT). The folder also includes an .xlsx file gathering all the relevant data and the measurements of precision and recall. Supplementary Data 9 (.zip file);  Detecting the temporal pattern of cell divisions in regenerating legs The data used to generate Figure 4 are contained in this compressed folder, including the five image datasets (.tif, .h5, .xml), the detected cell divisions (.mastodon files), and an .xlxs file containing all the cell divisions counts and graphs. Video 1.  Time lapse recording of regeneration in a Parhyale T5 leg (dataset li48-t5) Live imaging of nuclei labelled with H2B-mREFruby (maximum projection of z slices 3-10). Proximal parts of the leg are to the left and the amputation site is at the right of the frame. For annotations of different features please refer to Figure 2. Shortly after leg amputation (0 hpa) hemocytes adhere to the wound. By 16 hpa the wound has melanized. Up to ~32 hpa epithelial cells can be seen migrating and accumulating at the wound, below the melanized scab (Figure 2A,B). Around 31 hpa, the leg tissues become detached from the scab (Figure 2C). At 43 hpa, the carpus-propodus boundary first becomes visible, and thereafter many cells can be observed dividing at the distal part of the leg stump (Figure 2D). At 56 hpa, the propodus-dactylus boundary first becomes visible (Figure 2E). At later stages, tissues in more proximal parts of the leg retract, making space for the regenerating leg to grow (Figure 2F,G). After ~90 hpa cell proliferation there is less cell proliferation and cell movements, and the nuclear positions within the tissue become fixed. Scale bars, 20 µm. Video 2.  Time lapse recording of regeneration in a Parhyale T5 leg (dataset li36-t5) Live imaging of nuclei labelled with H2B-mREFruby (maximum projection of z slices 3-15). Proximal parts of the leg are to the left and the amputation site is at the right of the frame. The sequence of events is similar to that described in Video 1, but the progression is slower: epithelial migration towards the wound is observed up to 40 hpa, tissues detach from the scab at 65 hpa, and the carpus-propodus and propodus-dactylus boundaries first become visible at 78 and 91 hpa. The tissues making up the carpus and propodus can be seen pulsating from 105 to 145 hpa. Scale bars, 20 µm.

opencc-by-4.0Oct 2021View details →

MEaSUREs ITS_LIVE Sentinel-1 Image-Pair Glacier and Ice Sheet Surface Velocities: Version 2 (Greenland Sample Products)

We provide 21 sample products of MEaSUREs ITS_LIVE Sentinel-1 Image-Pair Glacier and Ice Sheet Surface Velocities: Version 2 in three test regions of Greenland Ice Sheet. The full archive of version 2 ITS_LIVE products (including image pair maps, data cubes and mosaics) from Sentinel-1 as well as other optical sensors (Landsat-4/5/6/7/8 and Sentinel-2) can be found at the ITS_LIVE project website: <a href="https://its-live.jpl.nasa.gov/">https://its-live.jpl.nasa.gov</a>. Sensor: Sentinel-1A/B Processor: <a href="https://github.com/isce-framework/isce2">ISCE</a>v2.4.1 (topsApp -> <a href="https://github.com/leiyangleon/Geogrid">Geogrid</a>v1.4.0 -> <a href="https://github.com/nasa-jpl/autoRIFT">autoRIFT</a>v1.4.0) Project: NASA MEaSUREs project <a href="https://its-live.jpl.nasa.gov">ITS_LIVE</a> Region 1 (69.13N, 50.88W; Jakobshavn Isbræ Glacier): 7 ascending image pairs Region 2 (77.61N, 42.79W; central north of interior Greenland): 3 ascending image pairs Region 3 (72.48N, 35.87W; central south of interior Greenland): 10 descending image pairs and 1 ascending image pair This serves as a supplementary dataset for the companion journal article submitted to Earth System Science Data (to appear).   Acknowledgement: This effort was funded by the NASA MEaSUREs program in contribution to the Inter-mission Time Series of Land Ice Velocity and Elevation (ITS_LIVE) project (<a href="https://its-live.jpl.nasa.gov/">https://its-live.jpl.nasa.gov/</a>) and through Alex Gardner’s participation in the NASA NISAR Science Team.

opencc-by-4.0Dec 2021View details →

Dynamics of CTCF and cohesin mediated chromatin looping revealed by live-cell imaging

Overview This repository contains all the raw and processed trajectory data associated with “paper title”. In this ReadMe file we provide the following information: <ul> <li>The cell lines and conditions used in this study</li> <li>A summary of how the data was collected</li> <li>The structure of the chromosome locus tracking data</li> </ul> Cell lines and conditions In total, the dataset covers 12 experimental conditions representing the following cell lines and treatment conditions: <ul> <li>C36</li> <li>C65</li> <li>C27</li> <li>CTCF-AID (untreated)</li> <li>CTCF-AID (2 hours AID)</li> <li>CTCF-AID (4 hours AID)</li> <li>RAD21-AID (untreated)</li> <li>RAD21-AID (2 hours AID)</li> <li>RAD21-AID (4 hours AID)</li> <li>WAPL-AID (untreated)</li> <li>WAPL-AID (4 hours AID)</li> <li>WAPL-AID (6 hours AID)</li> </ul>   Data and data processing Trajectories were obtained from 3D timeseries of mouse embryonic stem cell colonies in the conditions listed above using a LSM900 Airyscan 2 Zeiss microscope. For each movie we recorded 365 frames of 49.69 µm x 49.69 µm (584 x 584 pixels, pixel size: 0.085 µm by 0.085 µm), separated by an interval of 20 seconds for a total of just over 2 hours. 3D images were composed of 30 z-stacks separated by 0.25 µm, for a total height of 7.25 µm. Imaging was performed in two colors allowing the tracking of two arrays of fluorophores on Chromosome 18 near the Fbn2 gene. In all conditions, the fluorophore arrays were separated by 515 kb (except the C27 clone where separation was 10 kb). The 3D image time series were processed using ConnectTheDots: <a href="https://github.com/ahansenlab/connect_the_dots">https://github.com/ahansenlab/connect_the_dots</a> to obtain paired trajectories of chromosome loci over time. The trajectories have been corrected for chromatic shifts and aberrations. Data are provided in an “unfiltered” format (meaning that individual dot localizations were not quality control filtered) , or a filtered format (the same data set, but having undergone quality control). The filtered (quality controlled) trajectory data was used for all the quantitative analyses in the article “”. File names are formatted follows. <ul> <li>Quality controlled data have the structure: {Clone_and_condition_name}.tagged_set.tsv</li> <li>Unfiltered data have the structure: {Clone_and_condition_name}.unfiltered.tagged_set.tsv</li> </ul> For example, for RAD21-AID tagged clone, for imaging performed after two hours of protein degradation, the quality-controlled file name is: RAD21_2_hr.tagged_set.tsv. Please note that for all no-treatment conditions, we used “0 hours” as the tag. Thus, the RAD21 (untreated) becomes RAD21_0_hr.tagged_set.tsv.   Structure of Data The trajectory data are provided as tab-separated text files consisting of 10 columns. The column headers are: <ul> <li>id: a unique dot pair index</li> <li>t: the frame in which the dots were localized</li> <li>x: x-coordinate of the dot in the EGFP channel (units in µm)</li> <li>y: y-coordinate of the dot in the EGFP channel (units in µm)</li> <li>z: z-coordinate of the dot in the EGFP channel (units in µm)</li> <li>x2: x-coordinate of the dot in the mScarlet channel (units in µm)</li> <li>y2: y-coordinate of the dot in the mScarlet channel (units in µm)</li> <li>z2: z-coordinate of the dot in the mScarlet channel (units in µm)</li> <li>dist: 3D distance between the dots across channels (units in µm)</li> <li>movie_index: an identifier used to link the dot pair back to the raw image timeseries.</li> </ul>

opencc-by-4.0Jun 2022View details →

Spatiotemporal multiplexed immunofluorescence imaging of living cells and tissues with bioorthogonal cycling of fluorescent probes

Raw multichannel and/or Z-stack source data from time series images in TIF format to accompany publication of: Spatiotemporal multiplexed immunofluorescence imaging of living cells and tissues with bioorthogonal cycling of fluorescent probes Jina Ko1, Martin Wilkovitsch2, Juhyun Oh1, Rainer Kohler1, Evangelia Bolli1,3, Mikael J. Pittet1,3,4,5, Claudio Vinegoni1, David B. Sykes6,7, Hannes Mikula2, Ralph Weissleder1,8*, Jonathan C. T. Carlson1,7* 1 Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114  2 Institute of Applied Synthetic Chemistry, TU Wien, 1060 Vienna, Austria  3 Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland 4 Ludwig Institute for Cancer Research, Lausanne Branch, Switzerland 5 AGORA Cancer Center, Lausanne, Switzerland 6 Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA 7 Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA 8 Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115

opencc-by-4.0Feb 2024View details →

High resolution microsection images for: Common juniper, the oldest living non-clonal woody species across the tundra biome and the European continent

Two high resolution images of the stem section are available as .czi files. These images are from a living Juniperus communis L. branch from Abisko (Sweden) sampled in August 2021. These high-resolution photographs (2.89 pixel/μm) were created using Axio Scan 7, Zeiss, Germany.  One high resolution image of the same stem section is archived as a .tif file (49835x25587 pixels). This image is a composition of the two .czi images created using Axio Scan 7, Zeiss, with a reduced resolution and edited adding the ring-count reference points and the reference scale.

opencc-by-4.0Oct 2021View details →

Sample version 2.0 ITS_LIVE Sentinel-1 image pair product of ice velocity in Greenland

21 samples of version 2.0 ITS_LIVE Sentinel-1 image pair product of ice velocity in three test regions of Greenland Ice Sheet Sensor: Sentinel-1A/B Processor: <a href="https://github.com/isce-framework/isce2">ISCE</a> v2.4.1 (topsApp -> <a href="https://github.com/leiyangleon/Geogrid">Geogrid</a> v1.4.0 -> <a href="https://github.com/nasa-jpl/autoRIFT">autoRIFT</a> v1.4.0) Project: NASA MEaSUREs project <a href="https://its-live.jpl.nasa.gov">ITS_LIVE</a> Region 1 (69.13N, 50.88W; Jakobshavn Isbræ Glacier): 7 ascending image pairs Region 2 (77.61N, 42.79W; central north of interior Greenland): 3 ascending image pairs Region 3 (72.48N, 35.87W; central south of interior Greenland): 10 descending image pairs and 1 ascending image pair This serves as a supplementary dataset for the companion journal article submitted to Earth System Science Data (to appear soon).   Acknowledgement: This effort was funded by the NASA MEaSUREs program in contribution to the Inter-mission Time Series of Land Ice Velocity and Elevation (ITS_LIVE) project (<a href="https://its-live.jpl.nasa.gov/">https://its-live.jpl.nasa.gov/</a>) and through Alex Gardner’s participation in the NASA NISAR Science Team

dryad40/100

ThermoCyte: an inexpensive open-source temperature control system for in vitro live cell imaging

Live-cell imaging is a common technique in microscopy to investigate dynamic cellular behaviour and permits the accurate and relevant analysis of a wide range of cellular and tissue parameters, such as motility, cell division, wound healing responses, and calcium (Ca2+) signalling in cell lines, primary cell cultures, and ex vivo preparations. Furthermore, this can take place under many experimental conditions, making live-cell imaging indispensable for biological research. Systems which maintain cells at physiological conditions outside of a CO2 incubator are often bulky, expensive, and use proprietary components. Here we present an inexpensive, open-source temperature control system for in vitro live cell imaging. Our system 'ThermoCyte', which is constructed from standard electronic components, enables precise tuning, control, and logging of a temperature 'set point' for imaging cells at physiological temperature. We achieved stable thermal dynamics, with reliable temperature cycling and a standard deviation of 0.42°C over 1 hour. Furthermore, the device is modular in nature, and is adaptable to the researcher's specific needs. This represents simple, inexpensive, and reliable tool for laboratories to carry out custom live-cell imaging protocols, on a standard lab bench, at physiological temperature.

opencc-zeroNov 2023View details →

opencc-by-4.0Nov 2024View details →

Live-Cell Imaging of MCF10A Cells Treated with EGF or PBS

MCF10A cell culture and experimental procedures were conducted based on established methodologies (10.1038/s42003-022-03975-9). For routine maintenance and passaging, cells were cultured in a growth medium composed of DMEM/F12 (Invitrogen, #11330-032) supplemented with 5% horse serum (Sigma, #H1138), 20 ng/ml EGF (R&D Systems, #236-EG), 0.5 µg/ml hydrocortisone (Sigma, #H-4001), 100 ng/ml cholera toxin (Sigma, #C8052), 10 µg/ml insulin (Sigma, #I9278), and 1% Penicillin/Streptomycin (Invitrogen, #15070-063). For experiments involving EGF perturbation, a growth factor-free medium was prepared using DMEM/F12, 5% horse serum, 0.5 µg/ml hydrocortisone, 100 ng/ml cholera toxin, and 1% Pen/Strep. Cells were cultured to 50–80% confluency before being detached with 0.05% trypsin-EDTA (Thermo Fisher Scientific, #25300-054). Subsequently, 20,000 cells were seeded into 24-well plates (Thermo Fisher Scientific, #267062) coated with collagen-1 (Cultrex, #3442-050-01) in growth medium. After six hours, the cells were rinsed with PBS, and the medium was replaced with growth factor-free medium. Following an 18-hour period of growth factor deprivation, cells were treated with either PBS or 10 ng/ml EGF (R&D Systems, #236-EG). Phenotypic responses to EGF treatment were assessed through live-cell imaging using the Incucyte S3 microscope (Essen BioScience, #4647), which captured images every 30 minutes over a 24-hour period. The dataset includes an Excel spreadsheet that documents the experimental conditions for each imaged well.

opencc-by-4.0Mar 2022View details →

Live cell microscopy: From image to insight - raw data & analysis

Accompanying raw and processed data as well as analysis scripts for the publication Biophysics Rev. 3, (2022); <a href="https://doi.org/10.1063/5.0082799">10.1063/5.0082799</a>  "Live cell microscopy: From image to insight".

(10)-Strobl2022A-DS0008 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0008 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0004 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0004 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0001 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0001 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0003 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0003 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0002 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0002 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0007 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0007 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0009 – Ceratitis capitata TREhs43-hid^Ala5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy

(10)-Strobl2022A-DS0009 – Ceratitis capitata TREhs43-hidAla5_F1m2 long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy