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Data Analysis WorkbeNch (DAWN)

Journal of synchrotron radiation, 2015-05, Vol.22 (3), p.853-858

2015

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A high-throughput system for high-quality tomographic reconstruction of large datasets at Diamond Light Source

Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences, 2015-06, Vol.373 (2043), p.20140398

2015

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I12: the Joint Engineering, Environment and Processing (JEEP) beamline at Diamond Light Source

Journal of synchrotron radiation, 2015-05, Vol.22 (3), p.828-838

2015

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Thriving in Academia: Building a Career at a Teaching-Focused Institution

APA Books, 2021

2021

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Temporal refinement of 3D CNN semantic segmentations on 4D time-series of undersampled tomograms using hidden Markov models

Scientific reports, 2021-12, Vol.11 (1), p.23279-23279, Article 23279

2021

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High performance Savu software for fast 3D model-based iterative reconstruction of large data at Diamond Light Source

SoftwareX, 2022-07, Vol.19, p.101157, Article 101157

2022

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Cryo-plasma FIB/SEM volume imaging of biological specimens

eLife, 2023-02, Vol.12

2023

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RedLionfish - fast Richardson-Lucy Deconvolution package for efficient point spread function suppression in volumetric data

Wellcome open research, 2024, Vol.9, p.296

2024

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Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography

Open biology, 2021-10, Vol.11 (10), p.210160-210160

2021

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Comparison of Methods to Segment Variable-Contrast XCT Images of Methane-Bearing Sand Using U-Nets Trained on Single Dataset Sub-Volumes

Methane, 2022-12, Vol.2 (1), p.1-23

2022

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SuRVoS 2: Accelerating Annotation and Segmentation for Large Volumetric Bioimage Workflows Across Modalities and Scales

Frontiers in cell and developmental biology, 2022-04, Vol.10, p.842342-842342

2022

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Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow

Biological imaging (Cambridge, England), 2023, Vol.3, p.e10-e10, Article e10

2023

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Neuronal Migration Is Retarded in Mice Lacking the Tissue Plasminogen Activator Gene

Proceedings of the National Academy of Sciences - PNAS, 1999-11, Vol.96 (24), p.14118-14123

1999

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Okapi-EM: A napari plugin for processing and analyzing cryogenic serial focused ion beam/scanning electron microscopy images

Biological imaging (Cambridge, England), 2023, Vol.3, p.e9-e9, Article e9

2023

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Absence of Tissue Plasminogen Activator Gene or Activity Impairs Mouse Cerebellar Motor Learning

The Journal of neuroscience, 2003-08, Vol.23 (19), p.7368-7375

2003

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Can we predict T cell specificity with digital biology and machine learning?

Nature reviews. Immunology, 2023-08, Vol.23 (8), p.511-521

2023

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Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow

Biophysical journal, 2023-02, Vol.122 (3), p.462a-462a

2023

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CHiMP: deep‐learning tools trained on protein crystallization micrographs to enable automation of experiments

Acta crystallographica. Section D, Biological crystallography., 2024-10, Vol.80 (10), p.744-764

2024

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Using Artificial Immune Systems to Sort and Shim Insertion Devices at Diamond Light Source

Journal of physics. Conference series, 2022-12, Vol.2380 (1), p.12022

2022

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X‐ray tomographic reconstruction and segmentation pipeline for the long‐wavelength macromolecular crystallography beamline at Diamond Light Source

Journal of synchrotron radiation, 2021-05, Vol.28 (3), p.889-901

2021

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Pillar data‐acquisition strategies for cryo‐electron tomography of beam‐sensitive biological samples

Acta crystallographica. Section D, Biological crystallography., 2024-06, Vol.80 (6), p.421-438

2024

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Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples

Ultramicroscopy, 2024-02, Vol.256, p.113882-113882, Article 113882

2024

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A convolutional neural network for fast upsampling of undersampled tomograms in X‐ray CT time‐series using a representative highly sampled tomogram

Journal of synchrotron radiation, 2019-05, Vol.26 (3), p.839-853

2019

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Volume Segmantics: A Python Package for Semantic Segmentation of Volumetric Data Using Pre-trained PyTorch Deep Learning Models

Journal of open source software, 2022-10, Vol.7 (78), p.4691

2022

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A stacked dense denoising–segmentation network for undersampled tomograms and knowledge transfer using synthetic tomograms

Machine vision and applications, 2021-05, Vol.32 (3), Article 75

2021

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Data Analysis WorkbeNch (DAWN)

A high-throughput system for high-quality tomographic reconstruction of large datasets at Diamond Light Source

I12: the Joint Engineering, Environment and Processing (JEEP) beamline at Diamond Light Source

Thriving in Academia: Building a Career at a Teaching-Focused Institution

Temporal refinement of 3D CNN semantic segmentations on 4D time-series of undersampled tomograms using hidden Markov models

High performance Savu software for fast 3D model-based iterative reconstruction of large data at Diamond Light Source

Cryo-plasma FIB/SEM volume imaging of biological specimens

RedLionfish - fast Richardson-Lucy Deconvolution package for efficient point spread function suppression in volumetric data

Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography

Comparison of Methods to Segment Variable-Contrast XCT Images of Methane-Bearing Sand Using U-Nets Trained on Single Dataset Sub-Volumes

SuRVoS 2: Accelerating Annotation and Segmentation for Large Volumetric Bioimage Workflows Across Modalities and Scales

Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow

Neuronal Migration Is Retarded in Mice Lacking the Tissue Plasminogen Activator Gene

Okapi-EM: A napari plugin for processing and analyzing cryogenic serial focused ion beam/scanning electron microscopy images

Absence of Tissue Plasminogen Activator Gene or Activity Impairs Mouse Cerebellar Motor Learning

Can we predict T cell specificity with digital biology and machine learning?

Ot2Rec: A semi-automatic, extensible, multi-software tomographic reconstruction workflow

CHiMP: deep‐learning tools trained on protein crystallization micrographs to enable automation of experiments

Using Artificial Immune Systems to Sort and Shim Insertion Devices at Diamond Light Source

X‐ray tomographic reconstruction and segmentation pipeline for the long‐wavelength macromolecular crystallography beamline at Diamond Light Source

Pillar data‐acquisition strategies for cryo‐electron tomography of beam‐sensitive biological samples

Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples

A convolutional neural network for fast upsampling of undersampled tomograms in X‐ray CT time‐series using a representative highly sampled tomogram

Volume Segmantics: A Python Package for Semantic Segmentation of Volumetric Data Using Pre-trained PyTorch Deep Learning Models

A stacked dense denoising–segmentation network for undersampled tomograms and knowledge transfer using synthetic tomograms

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