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Intro
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CryoET data analysis offers many opportunities... but also present significant challenges
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Quantifying mitochondrial granules in HD neurons
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HD Patient iPSC-Derived Neurons on CryoEM Grids
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Objective: Automated Quantification of Mito Granules
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Training a 3D Segmentation Model
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Quantitative Characterization of Mitochondrial Granules in Neurites of HD Neurons
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Ongoing and Future Directions
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Further reducing annotation needs for training computer vision algorithms
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Unsupervised learning methods for segmentation
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Motivations for our work in unsupervised segmentation
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Hyperbolic space
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Poincare ball model
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Gyrovector operations bring linear algebra to the Poincare ball
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Our work: reconstructing visual hierarchy as a pretext task
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Self-supervised hierarchical triplet loss
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Hyperbolic clustering
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Experimental validation
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BraTS Dataset (Menze et al 2015)
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Cryogenic electron tomography
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Summary
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Domain adaptive unsupervised instance segmentation for biomedical images
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DARCNN: Domain Adaptive Region-based Convolutional Neural Network for Unsupervised Instance Segmentation in Biomedical Images
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Background: Mask R-CNN instance segmentation architecture
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DARCNN model: feature-level adaptation
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DARCNN model: pseudo-labelling
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Potential unsupervised discovery applications in Cryo-ET
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Developing Computer Vision Methods for Segmenting and Analyzing Subcellular Components in Cryo-ET
Description:
Explore computer vision methods for automated segmentation and analysis of subcellular components in cryo-electron tomography (cryoET) data. Delve into the challenges of analyzing 3D tomogram data and learn about approaches for segmenting mitochondrial volumes and granules in iPSC-derived neurons from Huntington's Disease patient samples. Discover ongoing research on label-efficient segmentation techniques to scale computer vision analysis to larger numbers of features. Examine the potential of unsupervised learning methods, including hyperbolic space models and domain adaptive region-based convolutional neural networks, for biomedical image segmentation. Gain insights into the future directions of computer vision applications in cryoET data analysis and their implications for understanding subcellular structures and interactions.

Computer Vision for Segmenting & Analyzing Subcellular Components in Cryo-Electron Tomography

Institute for Pure & Applied Mathematics (IPAM)
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