Oliver N. F. King
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View article: From Voxels to Viruses: Using Deep Learning and Crowdsourcing to Understand a Virus Factory
From Voxels to Viruses: Using Deep Learning and Crowdsourcing to Understand a Virus Factory Open
Many bioimaging research projects require objects of interest to be identified, located, and then traced to allow quantitative measurement. Depending on the complexity of the system and imaging, instance segmentation is often done manually…
View article: CHiMP: deep-learning tools trained on protein crystallization micrographs to enable automation of experiments
CHiMP: deep-learning tools trained on protein crystallization micrographs to enable automation of experiments Open
A group of three deep-learning tools, referred to collectively as CHiMP (Crystal Hits in My Plate), were created for analysis of micrographs of protein crystallization experiments at the Diamond Light Source (DLS) synchrotron, UK. The firs…
View article: CHiMP: Deep Learning Tools Trained on Protein Crystallisation Micrographs to Enable Automation of Experiments
CHiMP: Deep Learning Tools Trained on Protein Crystallisation Micrographs to Enable Automation of Experiments Open
A group of three deep learning tools, referred to collectively as CHiMP (Crystal Hits in My Plate) were created for analysis of micrographs of protein crystallisation experiments at the Diamond Light Source (DLS) synchrotron, UK. The first…
View article: Online citizen science with the Zooniverse for analysis of biological volumetric data
Online citizen science with the Zooniverse for analysis of biological volumetric data Open
Public participation in research, also known as citizen science, is being increasingly adopted for the analysis of biological volumetric data. Researchers working in this domain are applying online citizen science as a scalable distributed…
View article: Online citizen science with the Zooniverse for analysis of biological volumetric data
Online citizen science with the Zooniverse for analysis of biological volumetric data Open
Public participation in research, also known as citizen science, is being increasingly adopted for the analysis of biological volumetric data. Researchers working in this domain are applying online citizen science as a scalable distributed…
View article: Comparison of Methods to Segment Variable-Contrast XCT Images of Methane-Bearing Sand Using U-Nets Trained on Single Dataset Sub-Volumes
Comparison of Methods to Segment Variable-Contrast XCT Images of Methane-Bearing Sand Using U-Nets Trained on Single Dataset Sub-Volumes Open
Methane (CH4) hydrate dissociation and CH4 release are potential geohazards currently investigated using X-ray computed tomography (XCT). Image segmentation is an important data processing step for this type of research. However, it is oft…
View article: Volume Segmantics: A Python Package for SemanticSegmentation of Volumetric Data Using Pre-trained PyTorch Deep LearningModels
Volume Segmantics: A Python Package for SemanticSegmentation of Volumetric Data Using Pre-trained PyTorch Deep LearningModels Open
King et al., (2022). Volume Segmantics: A Python Package for Semantic Segmentation of Volumetric Data Using Pre-trained PyTorch Deep Learning Models. Journal of Open Source Software, 7(78), 4691, https://doi.org/10.21105/joss.04691
View article: U-Net Segmentation Methods for Variable-Contrast XCT Images of Methane-Bearing Sand Using Small Training Datasets
U-Net Segmentation Methods for Variable-Contrast XCT Images of Methane-Bearing Sand Using Small Training Datasets Open
Earth and Space Science Open Archive This preprint has been submitted to and is under consideration at Other. ESSOAr is a venue for early communication or feedback before peer review. Data may be preliminary.Learn more about preprints prep…
View article: SuRVoS 2: Accelerating Annotation and Segmentation for Large Volumetric Bioimage Workflows Across Modalities and Scales
SuRVoS 2: Accelerating Annotation and Segmentation for Large Volumetric Bioimage Workflows Across Modalities and Scales Open
As sample preparation and imaging techniques have expanded and improved to include a variety of options for larger sized and numbers of samples, the bottleneck in volumetric imaging is now data analysis. Annotation and segmentation are bot…
View article: Beamline K11 DIAD: a new instrument for dual imaging and diffraction at Diamond Light Source
Beamline K11 DIAD: a new instrument for dual imaging and diffraction at Diamond Light Source Open
The Dual Imaging and Diffraction (DIAD) beamline at Diamond Light Source is a new dual-beam instrument for full-field imaging/tomography and powder diffraction. This instrument provides the user community with the capability to dynamically…
View article: A massively multi-scale approach to characterizing tissue architecture by synchrotron micro-CT applied to the human placenta
A massively multi-scale approach to characterizing tissue architecture by synchrotron micro-CT applied to the human placenta Open
Multi-scale structural assessment of biological soft tissue is challenging but essential to gain insight into structure–function relationships of tissue/organ. Using the human placenta as an example, this study brings together sophisticate…
View article: U-Net Segmentation Methods for Variable-Contrast XCT Images of Methane-Bearing Sand
U-Net Segmentation Methods for Variable-Contrast XCT Images of Methane-Bearing Sand Open
Earth and Space Science Open Archive This preprint has been submitted to and is under consideration at Earth and Space Science. ESSOAr is a venue for early communication or feedback before peer review. Data may be preliminary.Learn more ab…
View article: Tomography data of methane-bearing sand used to investigate U-Net segmentation methods
Tomography data of methane-bearing sand used to investigate U-Net segmentation methods Open
These tomographic data sets were used to evaluate the suitability of different U-Net implementations to produce accurate segmentations. Hand-annotated training and validation sub-volumes as well as the segmentation outputs from the U-Net i…
View article: Tomography data of methane-bearing sand used to investigate U-Net segmentation methods
Tomography data of methane-bearing sand used to investigate U-Net segmentation methods Open
These tomographic data sets were used to evaluate the suitability of different U-Net implementations to produce accurate segmentations. Hand-annotated training and validation sub-volumes as well as the segmentation outputs from the U-Net i…
View article: A massively multi-scale approach to characterising tissue architecture by synchrotron micro-CT applied to the human placenta
A massively multi-scale approach to characterising tissue architecture by synchrotron micro-CT applied to the human placenta Open
Multi-scale structural assessment of biological soft tissue is challenging but essential to gain insight into structure-function relationships of tissue/organ. Using the human placenta as an example, this study brings together sophisticate…
View article: 2d U-net models trained to segment human placental maternal/fetal blood volumes and blood vessels from syncrotron micro-CT data along with a sample data volume.
2d U-net models trained to segment human placental maternal/fetal blood volumes and blood vessels from syncrotron micro-CT data along with a sample data volume. Open
This dataset contains a 512 x 512 x 512 pixel volume taken from an imaging dataset of human placental tissue collected at Diamond Light Source Manchester Imaging Branchline, I13-2 on visits MG23941 and MG22562 using in-line high-resolution…
View article: 2d U-net models trained to segment human placental maternal/fetal blood volumes and blood vessels from syncrotron micro-CT data along with a sample data volume.
2d U-net models trained to segment human placental maternal/fetal blood volumes and blood vessels from syncrotron micro-CT data along with a sample data volume. Open
This dataset contains a 512 x 512 x 512 pixel volume taken from an imaging dataset of human placental tissue collected at Diamond Light Source Manchester Imaging Branchline, I13-2 on visits MG23941 and MG22562 using in-line high-resolution…
View article: Free–Wilson Analysis of Comprehensive Data on Phosphoinositide-3-kinase (PI3K) Inhibitors Reveals Importance of <i>N</i>-Methylation for PI3Kδ Activity
Free–Wilson Analysis of Comprehensive Data on Phosphoinositide-3-kinase (PI3K) Inhibitors Reveals Importance of <i>N</i>-Methylation for PI3Kδ Activity Open
Phosphoinositide-3-kinase δ (PI3Kδ) is a critical regulator of cell growth and transformation and has been explored as a therapeutic target for a range of diseases. Through the exploration of the thienopyrimidine scaffold, we have identifi…
View article: Non-competitive cyclic peptides for targeting enzyme–substrate complexes
Non-competitive cyclic peptides for targeting enzyme–substrate complexes Open
Tight, non-active site binding cyclic peptides are promising affinity reagents for studying proteins and their interactions.