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35 results for “3D images analysis”
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>
Sample 3D image data from RIMS method for image analysis code demo
<p>Sample 3D image data from RIMS method applied to mechanical test on hydrogel sphere packings, to be used in image analysis code demo as demonstrated in the ALERT Geomechanics doctoral school 2022. The data is a small subset from a larger set of data as found on Dryad via 10.5061/dryad.6djh9w0x8 and is separated here on Zenodo to make the subset more machine-readable.</p>
Semi-Supervised Pre-trained Foundation Model for 3D Structural Feature Analysis of Seismic Images
<p>Codes, trained model, and datasets for the paper "Semi-Supervised Pre-trained Foundation Model for 3D Structural Feature Analysis of Seismic Images".</p>
BEHAV3D: A 3D live imaging platform for comprehensive analysis of engineered T cell behavior and tumor response
<p>The use of patient-derived material and immune cell co-cultures in modeling immune-oncology has gained significant interest for understanding and manipulating immune cell tumor targeting in a patient-specific context. However, current protocols have limitations in visualizing and analyzing the dynamic cellular features of these living culture systems. We recently developped a workflow names BEHAV3D, that combines multi-color live 3D imaging and computational tools to analyze cell death dynamics, classify T cell behavior, and generate data-informed 3D images and videos. Here we provide some example pre-processed dataset of videos of two co-culture set ups: breast cancer Patient Derived Organoids with αβ T cells engineered to express a γδ TCR (TEGs) and Acute Lymphoblastic Leukemia cells with CD19 CART cells.</p>
VesselExpress: Rapid and fully automated blood vasculature analysis in 3D light-sheet image volumes of different organs
<p>This dataset contains raw, segmented and skeletonized 3D light-sheet microscopic image volumes of blood vessels of different organs which were processed by VesselExpress. Please find the software here: https://github.com/RUB-Bioinf/VesselExpress. For details on how to run and setup the software please watch our tutorial (https://youtu.be/a8GWVKJNh68).</p>
Deep Learning-based 3D single-cell imaging analysis pipeline for quantifying cell-cell interaction dynamics in the tumor microenvironment
<p>These are 3D live-cell imaging datasets of gastric tumor organoids in co-culture with primary human Natural Killer (NK) cells. The datasets were analyzed by a new, deep learning-based 3D image analysis software tool, SiQ-3D, which we developed and presented in the paper titled "Deep Learning-based 3D single-cell imaging analysis pipeline for quantifying cell-cell interaction dynamics in the tumor microenvironment". Interested users can download the SiQ-3D software code from GitHub (https://github.com/simonlbd1/SiQ-3D) or Code Ocean (https://codeocean.com/capsule/6676007/tree/v2), analyze the 3D image datasets locally, and cross-check the results with the SiQ-3D quantified results that we provided here.</p>
BEHAV3D: A 3D live imaging platform for comprehensive analysis of engineered T cell behavior and tumor response
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3D micro-CT image of cichlid fish samples for genetic analysis
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Scripts and raw data for comparing 2D vs 3D image analysis of zebrafish embryo microscopic data
<p>Raw data and MatLab scripts used for image analysis of RNA polymerase II with serine 5 phosphorylation in the C-terminal domain (CTD) of the subunit 1 (Pol II Ser5P) in a fixed zebrafish embryo, comparing a 2D vs 3D approach to segment out the Pol II Ser5P clusters. Pol II Ser5P was labeled by immunofluorescence, microscopy images were acquired by instant-SIM microscopy and analyzed using MatLab scripts and the bioformats importer.</p>
In Situ Volumetric Imaging and Analysis of FRESH 3D Bioprinted Constructs Using Optical Coherence Tomography (Data and 3D models)
<p>These files contain 3D models and reconstructions of the 3D printed models after OCT imaging of the brain stem, circle of willis, kidney, vestibular apparatus, mixing network, and resolution text. These are from the journal article "In Situ Volumetric Imaging and Analysis of FRESH 3D Bioprinted Constructs Using Optical Coherence Tomography" published in <em>Biofabrication </em>(2022).</p>
Morphometric analysis of retinal ganglionic cells (3D confocal images) analyzed using filament tracer from Imaris software
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fMRI/fPACT 3D image stacks and analysis codes for function
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Figures 31-33 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 31-33 Quasicalathus, light microscopic images of the holotypes of Q. agonicollis sp. nov. (31.) and Q. conservans sp. nov. (32, 33.). 31. Ventral side of head showing chaetotaxy of mentum; 32. General view of the amber piece with fossil in dorsal view; 32. Left lateral view. Abbreviations: ce – compound eye; el – elytron; ems – external seta of submentum; gu – gula; ims – internal seta of submentum; msf – mesofemur; mt – mentum; mtf – metafemur; prf – profemur; pt – pronotum.
Figures 47-51 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 47-51 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimen "Groehn 7889". 47. Dorsal aspect; 48. Left lateral aspect; 49. Ventral aspect; 50. Pronotum (the arrows point to the insertions of the lateral setae); 51. Prosternum (for better view the prolegs are partly removed using the clipping plane function of Amira software. Abbreviations: cx – procoxa; psp – prosternal process; tr – protrochanter.
Figures 6-12 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 6-12 Quasicalathus elpis (Ortuño and Arillo 2009), light microscopic images of specimens "Groehn 7889" (6–8.) and "Groehn 7962" (9–12.). 6, 10. General view of the amber pieces (in Fig. 6, only the part of the large amber piece bearing the Quasicalathus fossil is shown); 7. Ventral side of body; 8. Left mesotarsi iv + v; 9. Pronotum and anterior part of elytra, left side of body; 11, 12. Medial part of left elytron (Fig. 12 shows the enlarged part of the elytron marked by the white frame in Fig. 11; the white arrow points to the insertion of the discal seta). Abbreviations: bs – insertion of the pronotal laterobasal seta; hm – humerus; I–VIII – elytral intervals 1–8.
Figures 34-38 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 34-38 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimens "Groehn 4879" (34–37.) and "Groehn 7814" (38.). 34. Dorsal aspect; 35. Right lateral aspect; 36. Ventral aspect; 37, 38. Prosternum and basal portions of prolegs. Abbreviations: cx – procoxa; fm – profemur; psp – prosternal process; tr – protrochanter.
Figures 81-89 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 81-89 Quasicalathus conservans sp. nov., volume rendering of the holotype. 81. Head, dorsal aspect (the arrows point to the insertions of the supraorbital setae); 82. Head, ventral aspect; 83. Left external part of metathorax, ventral view; 84. Submentum (the arrows point to the insertions of the four lateral setae); 85. Posterior part of prosternum and procoxae; 86. Posterior part of metasternum and metacoxae; 87–89. Preserved remains of the aedeagus (87. Right lateral aspect; 88. Dorsal aspect; 89. Left lateral aspect). Abbreviations: bb – basal bulb of aedeagal median lobe; ce – compound eye; cxp – metacoxal plate; eph – partly evaginated lobes of endophallus; gu – gula; mem – metepimeron; mes – metepisternum; mtt – mentum tooth; mv – metaventrite; pcx – procoxa; pmr –preserved distal part of right paramere of aedeagal median lobe; psp – prosternal process; sc – scutellum; sps – setae of sensory pit; tl – terminal lamella of aedeagal median lobe.
Figures 61-64 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 61-64 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimens "MAIG 76" (61–63.) and "GZG 16185" (64.); 61. Dorsal aspect; 62. Right lateral aspect; 63, 64. Pronotum (the pronotal outline on left side is highlighted by dotted line in Fig. 64).
Figures 39-46 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 39-46 Quasicalathus elpis (Ortuño and Arillo 2009), volume rendering of specimen "Groehn 7814" using different grey scales of the Amira software. 39. Dorsal aspect; 40. Lateral aspect. The displaced aedeagus (highlighted by red colour) was separated by the segmentation function of Amira software in Figures 39 and 40; 41. Head (the arrows point to the insertions of the supraorbital setae); 42. Pronotum (the arrows point to the insertions of the lateral setae); 43–46. Remains of the aedeagus in right lateral aspect (43.); Left lateral aspect (44.); Left lateral aspect (45.); Dorsal aspect (46.). The distal margins of the styloid apophysis of the right paramere in Fig. 43 and the lobate apophysis of the left paramere in Fig. 45 are highlighted by red dotted lines. Abbreviations: bb – basal bulb of aedeagal median lobe; os – distal ostium; pml – left paramere; pmr – right paramere; tl – terminal lamella of median lobe.
Figures 78-80 from: Schmidt J, Scholz S, Will K (2022) Character analysis and descriptions of Eocene sphodrine fossils (Coleoptera, Carabidae) using light microscopy, micro-CT scanning, and 3D imaging. Deutsche Entomologische Zeitschrift 69(1): 19-44. https://doi.org/10.3897/dez.69.79931
Figures 78-80 Quasicalathus conservans sp. nov., volume rendering of the holotype using different grey scales of the Amira software. 78. Dorsal aspect; 79. Left lateral aspect (aed – aedeagus); 80. Ventral aspect; the aedeagus (highlighted by red colour) was separated by the segmentation function of Amira software.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.