Mummering 3D Big Data Quantification

• 
• http://bit.ly/mumm3d

The material for the Big Data and 3D analysis presentation for the Mummering workshop on the analysis of large 3D/4D datasets.

Big Data

• Slides (static) Lecture Handout

• Applying Big Data Approaches to Tomography Data

• Old Video Recordings: Part 1 and Part 2

Supervised Analysis / Machine Learning (if time)

• Slides (static) Lecture Handout

Practical

Filtering and Image enhancement

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Fossils

The fossils example shows fossil data prepared by Phil Donoghue from the University of Bristol and published in Paleontology as The anatomy, taphonomy, taxonomy and systematic affinity of Markuelia: Early Cambrian to Early Ordovician scalidophorans

Dataset

• Small Fossils - https://www.kaggle.com/kmader/qbi-image-segmentation
• Odd Couple - https://www.kaggle.com/kmader/thrinaxodon-and-broomistega-3d-ct

Notebooks

• Viewing https://www.kaggle.com/kmader/teeth-fossil-viewing
• Viewing Couple https://www.kaggle.com/kmader/odd-couple-overview

Battery Analysis

The battery example comes from the group of Vanessa Woods from ETH Zurich and is published in X‐Ray Tomography of Porous, Transition Metal Oxide Based Lithium Ion Battery Electrodes

Dataset

https://www.kaggle.com/kmader/battery-3d-images

Notebooks

• Viewing https://www.kaggle.com/kmader/nmc-battery-3d-overview
• Segmentation / Watershed https://www.kaggle.com/kmader/battery-watershed-overview
• Texture Analysis https://www.kaggle.com/kmader/texture-to-detect-cracked-granules
• Parallel and Distributed Analysis https://www.kaggle.com/kmader/3d-image-analysis-using-dask

Foam analysis

These are datasets of cellular foam materials (water, aluminum) where the goal is to identify the distinct bubbles or cells in the foam.

Datasets

• Geology: https://github.com/kmader/conduit_analysis
• Aluminum: https://www.kaggle.com/rajmund/alufoam98 https://www.kaggle.com/rajmund/alufoam98t1
• Water Foams: https://www.kaggle.com/4quant/simplefoam

Corroding Paint

Dataset

• https://www.kaggle.com/4quant/painttomography

Medical CT images

Datasets

• Chest CT / Lungs - https://www.kaggle.com/kmader/finding-lungs-in-ct-data

Notebooks

• Overview: https://www.kaggle.com/kmader/data-preview
• Computer Vision Algorithm: https://www.kaggle.com/kmader/dsb-lung-segmentation-algorithm
• Simple Neural Network: https://www.kaggle.com/kmader/simple-nn-with-keras
• Lung U-Net Segmentation: https://www.kaggle.com/toregil/a-lung-u-net-in-keras

Hyperspectral Imaging

Dataset

• Time-series https://www.kaggle.com/kmader/circadian-rhythm-in-the-brain

Bonus Datasets

Electron Microscopy

https://www.kaggle.com/kmader/electron-microscopy-3d-segmentation

Bone Age with X-Rays

https://www.kaggle.com/kmader/rsna-bone-age