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209 results for “3D culture”
Images supporting: Nondestructive, quantitative viability analysis of 3D tissue cultures using machine learning image segmentation
<p>Two image datasets (as zip files) including all images analyzed in the manuscript Nondestructive, quantitative viability analysis of 3D tissue cultures using machine learning image segmentation. Images are of pancreatic adenocarcinoma (PDAC) cystic spheroid samples grown in either BME or Matrigel. Some images have background noise in the form of iron oxide nanoparticles introduced to them.</p>
Survival-associated cellular response maintained in pancreatic ductal adenocarcinoma (PDAC) switched between soft and stiff 3D microgel culture
<div> <div> <div> <div> <p>Pancreatic ductal adenocarcinoma (PDAC) accounts for about 90% of all pancreatic cancer cases. Five-year survival rates have remained below 12% since the 1970s, in part due to the difficulty in detection before metastasis (migration and invasion into neighboring organs and glands). Mechanical memory is a concept that has emerged over the past decade that may provide a path towards understanding how invading PDAC cells "remember" the mechanical properties of their diseased ("stiff," elastic modulus, E ≈ 10 kPa) microenvironment even whilst invading a healthy ("soft," E ≈ 1 kPa) microenvironment. Here, we investigated the role of mechanical priming by culturing a dilute suspension of PDAC (FG) cells within a 3D, rheologically tunable microgel platform from hydrogels with tunable mechanical properties. We conducted a suite of acute (short-term) priming studies where we cultured PDAC cells in either a soft (E ≈ 1 kPa) or stiff (E ≈ 10 kPa) environment for 6 h, then removed and placed them into a new soft or stiff 3D environment for another 18 h. Following these steps, we conducted RNA-seq analyses to quantify gene expression. Initial priming in 3D culture showed persistent gene expression for the duration of the study, regardless of the subsequent environments (stiff or soft). Stiff 3D culture was associated with the down-regulation of tumor suppressors (LATS1, BCAR3, CDKN2C ), as well as the up-regulation of cancer-associated genes (RAC3). Immunofluorescence staining (BCAR3, RAC3) further supported the persistence of this cellular response, with BCAR3 upregulated in soft culture, and RAC3 upregulated in stiff-primed culture. Stiff-primed genes were stratified against patient data found in The Cancer Genome Atlas (TCGA). Upregulated genes in stiff-primed 3D culture were associated with decreased survival in patient data, suggesting a link between patient survival and mechanical priming.</p> </div> </div> </div> </div>
Correlative microscopy of rat cultured hippocampal pyramidal cell from 40x confocal imaging to super-resolution 93x 3D STED of dendritic spines
<p>This dataset contain multi-scale image of rat hippocampal pyramidal cell related to our paper "<em>From tissues to segmentation: a modular framework for multi-scale neuron isolation</em>" by Cauzzo et al. <strong>Nature Comm (2024).</strong></p>
Prototyping 3D Virtual Learning Environments with X3D-based Content and Visualization Tools-Figure 11. Online accessible repository of digital data on cultural heritage with X3D models (STARC Web Repository, 2017, © Copyright 2017, STARC, Cyprus Institute. Used with permission)
<p>Prototyping can also include the development of toolkits for automatic content generation simulator, but in the case of an architectural environment, the components are too complex to be automatically generated. Furniture elements or the learning artifacts (i.e. content created by learners) can be converted to be viewed in X3D compatible browsers or included in online galleries (Figure 11). After functional and 3D content prototyping, certain components of the virtual campus can be easily modified and adapted as needed.</p>
Supplementary videos for the "Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture" manuscript
<p>Supplementary videos for preprint manuscript: </p> <p><em>Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture</em><br> Liuba Dvinskikh, Hugh Sparks, Liliana Brito, Kenneth T MacLeod, Sian E Harding, Christopher Dunsby<br> bioRxiv 2023.01.28.526043; doi: https://doi.org/10.1101/2023.01.28.526043</p> <p>All videos have been rendered with JPEG compression.</p> <p>Shortened video captions (Please see supplementary information document for full caption)<br> <strong>Video 1:</strong> 3D LSFM timelapse of hiPSC-CM undergoing spontaneous calcium transients. <br> <strong>Video 2:</strong> Widefield transillumination timelapse of hiPSC-CM and adult-CM <br> <strong>Video 3:</strong> Widefield fluorescence timelapse of hiPSC-CM and adult CM with synchronized spontaneous calcium transients. <br> <strong>Video 4a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients. <br> <strong>Video 4b</strong>: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients. <br> <strong>Video 5a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients in a sample without NBleb. <br> <strong>Video 5b</strong>: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture without NBleb undergoing synchronized spontaneous transients. <br> <strong>Video 6a</strong>: 3D LSFM timelapse of hiPSC-CM and adult-CM co-culture undergoing synchronized spontaneous transients in a sample treated with NBleb. <br> <strong>Video 6b:</strong> Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture with NBleb undergoing synchronized spontaneous transients. <br> <strong>Video 7a:</strong> 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture undergoing synchronized spontaneous transients in a sample without NBleb. <br> <strong>Video 7b: </strong>Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture without NBleb. </p> <p> </p>
Synthesis of large scale 3D microscopic images of 3D cell cultures for training and benchmarking
<p>Accompaning data to the paper:</p> <p>Synthesis of large scale 3D microscopic images of 3D cell cultures for training and benchmarking</p>
Survival-associated cellular response maintained in pancreatic ductal adenocarcinoma (PDAC) switched between soft and stiff 3D microgel culture
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3D co-culture of pleura
<p>Pleural mesothelial cells are the predominant cell type in the pleural cavity, but their role in the pathogenesis of pleural diseases needs to be further elucidated. 3D organotypic models are a encouraging approach for an <em>in vivo</em> understanding of molecular disease development. The aim of the present study was to develop a 3D organotypic model of the pleural mesothelium. Specimens of human <em>pleura parietalis</em> were obtained from patients undergoing surgery at the University Hospital Leipzig, Germany. 3D co-culture model of pleura was established from human pleural mesothelial cells and fibroblasts. The model was compared to human pleura tissue by phase-contrast and light microscopy, immunochemistry and -fluorescence as well as solute permeation test. Histological assessment of the 3D co-culture model displayed the presence of both cell types mimicking the morphology of the human pleura. Vimentin and Cytokeratin, PHD1 showed a similar expression pattern in pleural biopsies and 3D model. Expression of Ki-67 indicates the presence of proliferating cells. Tight junctional marker ZO-1 was found localized at contact zones between mesothelial cells. Each of these markers were expressed in both the 3D co-culture model and human biopsies. Permeability of 3D organotypic co-culture model of pleura was found to be higher for 70 kDa-Dextran and no significant difference was seen in the permeability for small dextran (4kDa). In summary, the presented 3D organoid of pleura functions as a robust assay for pleural research serving as a precise reproduction of the <em>in vivo</em> morphology and microenvironment.</p>
Remotely controlled 3D-engineered scaffolds for biomimetic in vitro investigations on brain cell co-cultures
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Driving cell response through deep learning, a study in simulated 3D cell cultures
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Supplementary Videos S1-S2 3D co-culture spheroid formation containing A498-ST cells
<p><strong>Supplementary Videos S1-S2</strong></p> <p><strong>3D co-culture spheroid formation containing A498-ST cells </strong></p> <p>Representative movies (<strong>S1</strong>, bright field and <strong>S2,</strong> fluorescence stained) recorded for 24 hours of an A498-ST 3D co-culture capturing the kinetic formation of a 3D spheroid. 3D co-cultures harbor 70% tumor cells (A498-ST, green), 20% fibroblasts (NHDFα, blue) and 10% endothelial cells (ECRF24, red). Scalebar represents 1000 µm. </p>
Culturing Patient-Derived Malignant Hematopoietic Stem Cells in Engineered and Fully Humanized 3D Niches
<p>Data underlying the figures in the publication “Culturing patient-derived malignant hematopoietic stem cells in engineered and fully humanized 3D niches”, published in <em>PNAS,</em><em> <strong>2021</strong>, 118 (40) e2114227118.</em></p> <p><em>DOI: 10.1073/pnas.2114227118</em></p> <p>Table of contents:</p> <p><strong>1. AML data_Gene expression</strong>: qPCR data related to AML samples.</p> <p><strong>2. AML data_Protein</strong>: Luminex data related to AML samples.</p> <p><strong>3. AML data_Supernatant vs Niche</strong>: FACS data comparing AML cells in the supernatant and niche compartments.</p> <p><strong>4. AML data_Supernatant</strong>: FACS data showing AML cells in the supernatant along the time.</p> <p><strong>5. Chemotherapy_2D_FACS</strong>: FACS data showing leukemic cell viability in 2D.</p> <p><strong>6. Chemotherapy_3D_FACS</strong>: FACS data showing leukemic cell viability in 3D (engineered niches).</p> <p><strong>7. MPN data</strong>: FACS data related to MPN samples.</p> <p><strong>8. SV-N_FACS</strong>: FACS data characterizing SV-N.</p> <p><strong>9. SV-N_Gene expression</strong>: qPCR data characterizing SV-N.</p> <p><strong>10. UCSD-AML1_Niche_FACS</strong>: FACS data showing UCSD-AML1 cells in the niche at final analysis.</p> <p><strong>11. UCSD-AML1_Niche_Gene expression</strong>: qPCR data showing UCSD-AML1 cells in the niche at final analysis.</p> <p><strong>12. UCSD-AML1_Supernatant_FACS</strong>: FACS data showing UCSD-AML1 cells in the supernatant along the time.</p> <p><strong>13. UCSD-AML1_Supernatant_Gene expression</strong>: qPCR data related to UCSD-AML1 cells in the supernatant along the time.</p> <p><strong>14. UCSD-AML1_Supernatant_Protein</strong>: Luminex data related to UCSD-AML1 cells in the supernatant along the time.</p> <p><strong>15. Images engineered niches</strong>: Zip archive containing images of engineered niches.</p>
Dataset comparing 2D and 3D culture for the calibration/validation of computational models
<p>Dataset comparing invasion adhesion and response to cisplatin and paclitaxel measured in PEO4 cells maintained either in 2D or 3D.</p> <p>Paper submitted to PLOS Computational Biology</p>
Fig. 7. Superimposed 3D in Structure and activity of a novel robust peroxidase from Alkanna frigida cell culture
Fig. 7. Superimposed 3D structure of HRP-C (in brown) on A) 1AP2 and B) POXalf. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Evaluation of low-intensity pulsed ultrasound on doxorubicin delivery in 2D and 3D cancer cell cultures
<p>This data set includes raw data supporting the paper "<strong>Evaluation of low-intensity pulsed ultrasound on doxorubicin delivery in 2D and 3D cancer cell cultures </strong>".</p> <p><strong>The files include the following data</strong>:</p> <p>1. The raw data used for calculating <strong>doxorubicin penetration </strong>in <strong>2D</strong> cancer cells;</p> <p>2. The raw data used for calculating <strong>doxorubicin</strong> <strong>penetration </strong>into tumor spheroids (<strong>3D</strong> cultures).</p>
Data from: Functional and mechanistic neurotoxicity profiling using human iPSC–derived neural 3D cultures
Neurological disorders affect millions of people worldwide and appear to be on the rise. While the reason for this increase remains unknown, environmental factors are a suspected contributor. Hence, there is an urgent need to develop more complex, biologically relevant, and predictive in vitro assays to screen larger sets of compounds with the potential for neurotoxicity. Here, we employed a human induced pluripotent stem cell (iPSC)-based 3D neural platform composed of mature cortical neurons and astrocytes as a model for this purpose. The iPSC-derived human 3D cortical neuron/astrocyte co-cultures (3D neural cultures) present spontaneous synchronized, readily detectable calcium oscillations. This advanced neural platform was optimized for high-throughput screening in 384-well plates and displays highly consistent, functional performance across different wells and plates. Characterization of oscillation profiles in 3D neural cultures was performed through multi-parametric analysis that included the calcium oscillation rate and peak width, amplitude, and waveform irregularities. Cellular and mitochondrial toxicity were assessed by high-content imaging. For assay characterization, we used a set of neuromodulators with known mechanisms of action. We then explored the neurotoxic profile of a library of 87 compounds that included pharmaceutical drugs, pesticides, flame retardants, and other chemicals. Our results demonstrated that 57% of the tested compounds exhibited effects in the assay. The compounds were then ranked according to their effective concentrations based on in vitro activity. Our results show that a human iPSC-derived 3D neural culture assay platform is a promising biologically-relevant tool to assess the neurotoxic potential of drugs and environmental toxicants.
Raw data for the article: 3D Culture and Interferon-? Priming Modulates Characteristics of Mesenchymal Stromal/Stem Cells by Modifying the Expression of Both Intracellular and Exosomal microRNAs
<p>Mesenchymal stromal/stem cells (MSCs) have emerged as a therapeutic tool in regenerative medicine. Recent studies have shown that exosome (EXO)-derived microRNAs (miRNAs) play a crucial role in mediating MSC functions. Additionally, intracellular miRNAs have been found to regulate MSC therapeutic capacities. However, the molecular mechanisms underlying miRNA-mediated MSC effects are not fully understood. We used 3D culture and IFN-γ to prime/enhance the MSC therapeutic effects in terms of functional miRNAs. After priming, our analysis revealed stable variations in intracellular miRNA among the MSC biological replicates. Conversely, a significant variability of miRNA was observed among EXOs released from biological replicates of the priming treatment. For each priming, we observed distinct miRNA expression profiles between the MSCs and their EXOs. Moreover, in both types of priming, gene ontology (GO) analysis of deregulated miRNAs highlighted their involvement in tissue repair/regeneration pathways. In particular, the 3D culture enhanced angiogenic properties in both MSCs and EXOs, while IFN-γ treatment enriched miRNAs associated with immunomodulatory pathways. These findings suggest that 3D culture and IFN-γ treatment are promising strategies for enhancing the therapeutic potential of MSCs by modulating miRNA expression. Additionally, the identified miRNAs may contribute to understanding the molecular mechanisms underlying the miRNA-mediated therapeutic effects of MSCs.</p>
Collaborative annotation of 3D digital cultural heritage: A new FOSS toolchain
<p>A suite of tools for semantic annotation of 3D cultural artefacts is being developed as part of the <a href="https://nfdi4culture.de/">NFDI4Culture</a> project across several partner organisations (led by the <a href="https://www.tib.eu/de/forschung-entwicklung/forschungsgruppen-und-labs/open-science">Open Science Lab at TIB, Hannover</a>). Operating within Task area 1: Data capture and enrichment, the proposed toolchain focuses on the annotation of 3D data within an open knowledge graph environment, so that 3D objects’ metadata and related annotations can be linked to various resources, part of the semantic web and all data is searchable via a public SPARQL endpoint. </p>
Effect of 3D Synthetic Microscaffold Nichoid on the Morphology of Cultured Hippocampal Neurons and Astrocytes
<p>The dataset contains the raw data and images of the paper.</p>
Data from: Functional and mechanistic neurotoxicity profiling using human iPSC–derived neural 3D cultures
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.