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Differential interference contrast (DIC) image of unstained living HepG2 human liver cancer cells
<p><strong>Introduction</strong></p> <p>This dataset is associated with our submission to Computers in Biology and Medicine, titled "Accurate Detection and Instance Segmentation of Unstained Living Adherent Cells in Differential Interference Contrast Images". The submission number for this manuscript is CIBM-D-23-09623R1.</p> <p><strong>Authors</strong>: Fei Pan, Yutong Wu, Kangning Cui, Shuxun Chen, Yanfang Li, Yaofang Liu, Adnan Shakoor, Han Zhao, Beijia Lu, Shaohua Zhi, Raymond Hon-Fu Chan, Dong Sun</p> <p><strong>Dataset Description</strong></p> <p>Our dataset comprises 520 differential interference contrast (DIC) images of 12,198 unstained HepG2 human liver cancer cells, each with a corresponding fluorescence image stained with calcein acetoxymethyl (AM), ensuring high-quality ground-truth annotations. Unique in addressing the multi-state nature of adherent cells commonly seen in wet labs, it includes both healthy and unhealthy cells in a single image, providing a valuable resource for studying multi-state cell detection and instance segmentation.<br>Citation</p> <p>We kindly request that researchers who use this dataset cite both our paper and this dataset. This will help acknowledge the work and facilitate further advancements in the field.</p> <p><br><strong>Please cite as follows:</strong></p> <p><strong>Paper:</strong><br>Pan, F., Wu, Y., Cui, K., Chen, S., Li, Y., Liu, Y., Shakoor, A., Zhao, H., Lu, B., Zhi, S., Chan, R. H.-F., & Sun, D. "Accurate detection and instance segmentation of unstained living adherent cells in differential interference contrast images,” <em>Computers in Biology and Medicine</em>, vol. 182, p. 109151, Nov. 2024, doi: 10/g5p9d8.</p> <p><strong>Dataset:</strong><br>Pan, F., Chen, S., Li, Y., Shakoor, A., Zhao, H., & Sun, D. (2024). Differential interference contrast (DIC) image of unstained living HepG2 human liver cancer cells. Zenodo. </p> <p>Thank you for your interest and support in our work. We look forward to seeing the innovative research that this dataset will enable.</p> <p> </p> <p> </p>
The Maintenance of Long-Lived Concentric Eyewall in Simulated Typhoon Lekima (2019)
<p>The model-simulated data used in this study are uploaded here. Due to the large number, the original simulation data are available on request (qnn_nancy@yahoo.com).</p>
WP2 T2.4 MEDIA T07 Live pilot 2 raw files, Cyclocross Soudal Leuven
<p>Two zip files - Directive and Omnidirectional. Inside the first one there is a proxy file of the TV broadcast of the filmed cyclocross men’s elite race. The zip file Omni has the 4 cameras and their respective raw files, that would require further editing to create a product in the form of a simulated live cyclocross experience, using either the ImmersiaTV plug-in or Cinegy Live.</p>
Microscopy images and movies supporting the publication: "tRNA tracking for direct measurements of protein synthesis kinetics in live cells"
<p>This repository contains experimental and simulated microscopy movies and images supporting the publication: Volkov et al. (2018) tRNA tracking for direct measurements of protein synthesis kinetics in live cells. <em>Nat Chem Biol, </em>DOI: 10.1038/s41589-018-0063-y</p> <p>A detailed list of files and file organisation can be found in Repository_content.pdf.</p>
Figure 3. Stylopallene tubirostris, A, B, male, dorsal and lateral views of trunk; C, female, anterior view of cephalon; D, scape process; E, live specimen; F, juveniles on male; G, juvenile; H, exuviae attached to male oviger.
Figure 3. Stylopallene tubirostris, A, B, male, dorsal and lateral views of trunk; C, female, anterior view of cephalon; D, scape process; E, live specimen; F, juveniles on male; G, juvenile; H, exuviae attached to male oviger.
Figure 1. Stylopallene cheilorhynchus, A, B, male, dorsal and lateral views of trunk; C, female, anterior view; D, live specimen; E, protonymphon on ovigers; F, discarded exuvia.
Figure 1. Stylopallene cheilorhynchus, A, B, male, dorsal and lateral views of trunk; C, female, anterior view; D, live specimen; E, protonymphon on ovigers; F, discarded exuvia.
Supplementary materials. Live traffic. Exploring Tehran with excitable medium
<p>These are videos of traffic in Tehran, used to analyse patterns of excitation on street network of Tehran. These are supplementary materials to the paper </p> <p>Exploring Tehran with excitable medium </p> <p>An excitable chemical medium --- Belousov-Zhabotinsky (BZ) reaction --- is proven to be a fruitful substrate for prototyping unconventional computing devices ~\cite{adamatzky2017east}. These include image processors, logical circuits, and robot controllers. We study a BZ potential for characterising a geometry of street networks on a fragment of Tehran street map. The city was chosen because it is one of the most populated cities in the World with nearly uncontrollable urban growth. In numerical experiments with Oregonator model of BZ reaction, we demonstrate that excitability of the medium allows acts as a selector between omnidirectional waves and soliton-like localised excitations. We uncover a phase-transition like dynamics, controlled by the excitability, of coverage of the street network by excitation wave-fronts. In the cluster analysis, we show how the network geometry, when it meets propagation of BZ wave-front, relates to the traffic flow of Tehran</p>
Skeletomuscular adaptations of head and legs of Melissotarsus ants for tunnelling through living wood
<p>Micro-CT raw datasets (in DICOM format) used in "Skeletomuscular adaptations of head and legs of Melissotarsus ants for tunnelling through living wood"</p> <p> </p> <p><strong>Abstract:</strong></p> <p>Background: While thousands of ant species are arboreal, very few are able to chew and tunnel through living wood. Ants of the genus <em>Melissotarsus</em> (subfamily Myrmicinae) inhabit tunnel systems excavated under the bark of living trees, where they keep large numbers of symbiotic armoured scale insects (family Diaspididae). Construction of these tunnels by chewing through healthy wood requires tremendous power, but the adaptations that give <em>Melissotarsus</em> these abilities are unclear. Here, we investigate the morphology of the musculoskeletal system of <em>Melissotarsus</em> using histology, scanning electron microscopy, X-ray spectrometry, X-ray microcomputed tomography (micro-CT), and 3D modelling.</p> <p>Results: Both the head and legs of <em>Melissotarsus</em> workers contain novel skeletomuscular adaptations to increase their ability to tunnel through living wood. The head is greatly enlarged dorsoventrally, with large mandibular closer muscles occupying most of the dorsal half of the head cavity, while ventrally-located opener muscles are also exceptionally large. This differs from the strong closing: opening asymmetry typical of most mandibulated animals, where closing the mandibles requires more force than opening. Furthermore, the mandibles are short and cone-shaped with a wide articulatory base that concentrates the force generated by the muscles towards the tips. The increased distance between the axis of mandibular rotation and the points of muscle insertion provides a mechanical advantage that amplifies the force from the closer and opener muscles. We suggest that the uncommonly strong opening action is required to move away crushed plant tissues during tunnelling and allow a steady forward motion. X-ray spectrometry showed that the tip of the mandibles is reinforced with zinc. Workers in this genus have aberrant legs, including mid- and hindlegs with hypertrophied coxae and stout basitarsi equipped with peg-like setae, and midleg femura pointed upward and close to the body. This unusual design famously prevents them from standing and walking on a normal two-dimensional surface. We reinterpret these unique traits as modifications to brace the body during tunnelling rather than locomotion per se.</p> <p>Conclusions: <em>Melissotarsus</em> represents an extraordinary case study of how the adaptation to – and indeed engineering of – a novel ecological niche can lead to the evolutionary redesign of core biomechanical systems.</p>
Results of questionnaire on live plant health nematode collections
<p>In the framework of the Euphresco project 2016-F-186 'Inventory of living collections of cyst and root knot nematodes in Europe and their maintenance techniques (Cyst and Melo Collect)', a survey was organised during the Autumn 2017 with the aim to collect information on the live nematode collections in different countries. 32 (reference) collections in Austria, Belgium, Canada, Czech Republic, France, Germany, Italy, Latvia, Mexico, Netherlands, Portugal, Spain, United Kingdom, and United States of America participated in the survey.</p> <p>Of the 32 mentioned collections the preferred nematode populations are clearly different between the USA and Europe: the tropical <em>Meloidogyne</em> species are the most represented in North America while <em>Globodera</em> species are in Europe.</p> <p>The comparison of the protocols for live nematode storage for short and long periods of time showed high variability, although in general, <em>Globodera</em> spp. can be stored at 4 °C for longer time (>20 years) than <em>Meloidogyne</em> spp., whose optimal storage time is 8 months at 14 °C, when kept in soil.</p> <p>The need to verify the population for its trueness, with other words, the frequency of identification differs; various possibilities are mentioned between never and almost monthly to frequently, each time the nematodes are extracted from the soil (90 days for PCN, 16 weeks for <em>Meloidogyne</em>) to yearly or only upon arrival. The frequency depends on the amount of time people can afford to put into this work and the risk assessment for getting cross contamination.</p> <p>The conditions for rearing and maintaining were inventoried as well. For <em>Meloidogyne</em> spp., host differences for rearing and maintaining them are rarely observed (often <em>Solanum lycopersicum</em> -tomato- is used for both), although <em>Ficus carina</em> for long maintenance of <em>Meloidogyne</em> spp. and <em>Solanum dulcamara</em> for <em>M. fallax</em> have been used in France (pers. comm. Fabrice Ollivier, ANSES). For cyst nematode species their specific host is used for both rearing and maintenance purposes: <em>Solanum tuberosum</em> (potato), <em>Nicotiana tabacum</em> (tobacco), or <em>Glycine max</em> (soybean) are used respectively for the potato cyst nematodes (<em>Globodera rostochiensis</em> and <em>G. pallida</em>), <em>G. tabacum</em> and <em>G. glycines</em>.</p> <p>The project report is also available on Zenodo https://zenodo.org/record/1442881#.W7PaxmgzbIU</p>
WP2 T2.4 MEDIA T12 Live pilot 3, MNM radio studio, visual radio pilot
<p> Live pilot 3, MNM radio studio, visual radio pilot</p> <p>3 files:<br> mnm-360-1.mp4: host of the show view<br> mnm-360-2.mp4: total view of the studio<br> mnm-360-3.mp4: dashboard of the host<br> </p> <p> </p>
Quantitative Characterisation of α-Synuclein Aggregation in Living Cells through Automated Microfluidics Feedback Control
<p>Data, computational software, and supplemental movies generated in the study: "Quantitative Characterisation of α-Synuclein Aggregation in Living Cells through Automated Microfluidics Feedback Control."</p>
Fast and Luminous Transients from the Explosions of Long-lived Massive White Dwarf Merger Remnants
<p>MESA inlists and run_star_extras associated with <a href="https://ui.adsabs.harvard.edu/?#abs/2017ApJ...850..127B">Brooks et al. (2017)</a>. MESA version 9793.</p> <p>Publication DOI: <a href="https://doi.org/10.3847/1538-4357/aa9568">10.3847/1538-4357/aa9568</a></p>
Data from: Heritability of growth and leaf loss compensation in a long-lived tropical understorey palm
<p>Data from: Heritability of growth and leaf loss compensation in a long-lived tropical understorey palm, PLOS ONE.</p> <p>Quantitative genetic data related to growth parameters and leaf loss compensation of 1402 <em>Chamaedorea elegans</em> seedlings. Data was collected in a greenhouse experiment performed at the Unifarm experimental facilities of Wageningen University between January 2013 and July 2014, in which a defoliation treatment was applied. Seeds were collected in the Montes Azules Biosphere Reserve in Chiapas, Mexico. See PLOS ONE publication for more details.</p> <p>The file contains a separate "read me" tab in which the meaning of the variable codes is explained. </p> <p> </p>
(06)-He2019A-DS0001 – Tribolium castaneum foxQ2-5' line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy
<p>(06)-He2019A-DS0001 – <em>Tribolium castaneum</em> foxQ2-5' line long-term live imaging dataset of embryonic development acquired with light sheet fluorescence microscopy</p>
Influence of environmental conditions on the fusion of cationic liposomes with living mammalian cells
<p>Lipid-based nanoparticles, also called vesicles or liposomes, can be used as carriers for drugs or many types of biological macromolecules including DNA and proteins. Efficiency and speed of cargo delivery are especially high for carrier vesicles that fuse with the cellular plasma membrane. This occurs for lipid mixture containing equal amounts of the cationic lipid DOTAP and a neutral lipid with an additional few percent of an aromatic substance. The fusion ability of such particles depends on lipid composition with phosphoethanolamine (PE) lipids favoring fusion and phosphatidyl-choline (PC) lipids endocytosis. Here we examined the effects of temperature, ionic strength, osmolality, and pH on fusion efficiency of cationic liposomes with Chinese hamster ovary (CHO) cells. The phase state of liposomes was analyzed by small angle neutron scattering (SANS). Our results showed that PC containing lipid membranes were organized in the lamellar phase. Here, fusion efficiency depended on buffer conditions and remained vanishingly small at physiological conditions. In contrast, SANS indicated the coexistence of very small (~ 50 nm) objects with larger, most likely lamellar structures for PE containing lipid particles. The fusion of such particles to cell membranes occurred with very high efficiency at all buffer conditions. We hypothesize that the altered phase state resulted in a highly reduced energetic barrier against fusion.</p>
Fig. 5 in Parasite burden in a short-lived chameleon, Furcifer labordi
Fig. 5. Intensity of mite infestation in adult F. labordi and F. cf. nicosiai.
Fig. 3 in Parasite burden in a short-lived chameleon, Furcifer labordi
Fig. 3. Prevalence of filarial infection in F. labordi and F. cf. nicosiai.
Figure 1 in Studies on the free-living protozoan fauna of estuaries in the coastal zone of Tamil Nadu, India
Figure 1. Map showing the localities of various estuaries studied for protozoan fauna.
Figure 20 in Free-living marine nematodes in Andhra Pradesh Coast, India
Figure 20 Paracanthonchus heterodontus.
Figure 19 in Free-living marine nematodes in Andhra Pradesh Coast, India
Figure 19. Epsilonema pustulatum.
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.