This dataset contains all data underlying the work presented in the linked Geotechnique journal publication. It contains the result of all experimental work described, as well as all numerical code (mixture of MATLAB, Python and R code) and numerical predictions for all computational models described.

The incidence of cutaneous squamous cell carcinoma (SCC) has increased in recent years, while it remains as an understudied subject. Current methods for the diagnose of skin cancer are either invasive, present a low resolution, or images that are difficult to interpret. Full-field optical coherence tomography (FF-OCT) has proven its potential as a non-invasive imaging technique of epithelial tissue. The sub-micrometer resolution offered by FF-OCT is able to show fine features such as cell nuclei,...

Drug resistance threatens the effective prevention and treatment of an ever-increasing range of human infections. This highlights an urgent need for new and improved drugs with novel mechanisms of action to avoid cross-resistance. Current cell-based drug screens are, however, restricted to binary live/dead readouts with no provision for mechanism of action prediction. Machine learning methods are increasingly being used to improve information extraction from imaging data. Such methods, however, work poorly with heterogeneous cellular phenotypes...

Libraries composed of 789,011 and 523,319 optically validated reference confocal micrographs of 17 and 20 EGFP fusion proteins localized at key cell organelles as landmarks in murine and human cells were generated for assignment of subcellular localization in mammalian cells. For each image of individual cells, 160 morphology and statistical features were used to train a random forests classifier to automatically assign the localization of proteins and dyes in both cell types and to analyze...

Libraries composed of 789,011 and 523,319 optically validated reference confocal micrographs of 17 and 20 EGFP fusion proteins localized at key cell organelles as landmarks in murine and human cells were generated for assignment of subcellular localization in mammalian cells. For each image of individual cells, 160 morphology and statistical features were used to train a random forests classifier to automatically assign the localization of proteins and dyes in both cell types and to analyze...

Libraries composed of 789,011 and 523,319 optically validated reference confocal micrographs of 17 and 20 EGFP fusion proteins localized at key cell organelles as landmarks in murine and human cells were generated for assignment of subcellular localization in mammalian cells. For each image of individual cells, 160 morphology and statistical features were used to train a random forests classifier to automatically assign the localization of proteins and dyes in both cell types and to analyze...

Recent evidence suggests that groups of cells are more likely to form clinically dangerous metastatic tumors, emphasizing the importance of understanding mechanisms underlying collective behavior. The emergent collective behavior of migrating cell sheets in vitro has been shown to be disrupted in tumorigenic cells but the connection between this behavior and in vivo tumorigenicity remains unclear. We use particle image velocimetry to measure a multidimensional migration phenotype for genetically defined human breast epithelial cell lines...

Dataset of 2718 raw images taken for the study of transfer and persistence of UV powder deposited on a variety of clothing material. This dataset constitutes a ground truth for use as a model for forensic trace evidence.

Recent evidence suggests that groups of cells are more likely to form clinically dangerous metastatic tumors, emphasizing the importance of understanding mechanisms underlying collective behavior. The emergent collective behavior of migrating cell sheets in vitro has been shown to be disrupted in tumorigenic cells but the connection between this behavior and in vivo tumorigenicity remains unclear. We use particle image velocimetry to measure a multidimensional migration phenotype for genetically defined human breast epithelial cell lines...

We explored the power of 3D super-resolution microscopy combined with computational classification and averaging to explore the 3D structure of the NPC in single human cells. We show that this approach can build the first integrated 3D structural map containing both central as well as peripheral NPC subunits with molecular specificity and nanoscale resolution. Our unbiased classification of over ten thousand individual NPCs indicates that the nuclear ring and the nuclear basket can adopt different...

Vegetation is a potential indicator of land contaminated by hydrocarbons. Remote sensing holds great potential for detecting stress in vegetation caused by the presence of hydrocarbons, but as yet this potential has not been realised, largely due to a lack of understanding of the biophysiological impacts of hydrocarbons on plant growth, and the specific spectral expression of them. Previous research has demonstrated success in laboratory simulation of hydrocarbon contamination and the analysis of the spectral...

Gene expression studies in early human development from 3 to 19 post conceptional weeks (PCW).

The coordination of cell movements across spatio-temporal scales ensures precise positioning of organs during vertebrate gastrulation. Mechanisms governing such morphogenetic movements have been studied only within a local region, a single germlayer or in whole embryos without cell identity. Scale-bridging imaging and automated analysis of cell dynamics are needed for a deeper understanding of tissue formation during gastrulation. Here we report pan-embryo analyses of formation and dynamics of all three germlayers simultaneously within a developing...

Away from the Mouse H&E quantification, the current version of MarrowQuant was tested on a small set of H&E bone marrow biopsies from anonymised patients. The tool performs in a comparable way as compared to the gold standard (Pathologists’ scorings), but it needs many optimisations before validating at the level of the human bone marrow biopsies quantifications and in clinical context.

This dataset contains the semen parameters of a fertile man, who have achieved a pregnancy in ≤ 12 months of trying to conceive, with an abstinence period of 2-7 days, at time of semen analysis. The parameters of a semen analysis included are; Semen Volume (ml), Sperm concentration(10x6 per ml), Total sperm number (10x6 per ejaculate), Total motility (PR + NP, %), Progressive motility (PR, %), Non-progressive motility (NP, %), Immotile spermatozoa (IM, %), Vitality...

Understanding genome organization requires integration of DNA sequence and 3D spatial context, however, existing genome-wide methods lack either base-pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across...

This dataset contains qualitative interview data which investigated interdisciplinary collaboration between sciences and the arts (with some other broad themes for comparative analysis). Participants from the discursive group interviews were staff members at the University of Dundee (UoD) involved in the doctoral research this dataset is related to. Participants from the informal interviews were not connected to the research directly or staff of the UoD, to allow comparative analysis methods to be conducted. The dataset...

Autoimmune β-cell destruction leads to type 1 diabetes, but the pathophysiological mechanisms remain unclear. To help address this void, we created an open-access online repository composed of large-scale electron microscopy images (‘nanotomy’) of human pancreas tissue obtained from the Network for Pancreatic Organ donors with Diabetes (nPOD; www.nanotomy.org). Nanotomy allows analyses of complete donor islets with up to macromolecular resolution. Our first results of mining the database support recent findings that suggest that type 1...

Xist RNA directs the process of X-chromosome inactivation in mammals by spreading in cis along the chromosome from which it is transcribed and recruiting chromatin modifiers to silence gene transcription. To elucidate mechanisms of Xist RNA cis-confinement, we established a sequential dual-color labeling, super-resolution imaging approach to trace individual Xist RNA molecules over time, enabling us to define fundamental parameters of spreading. We demonstrate a feedback mechanism linking Xist RNA synthesis and degradation, and an...