AIMC Topic: Organoids

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Deep-learning analysis of micropattern-based organoids enables high-throughput drug screening of Huntington's disease models.

Cell reports methods Sep 19, 2022
Organoids are carrying the promise of modeling complex disease phenotypes and serving as a powerful basis for unbiased drug screens, potentially offering a more efficient drug-discovery route. However, unsolved technical bottlenecks of reproducibilit...
Drug Evaluation, Preclinical High-Throughput Screening Assays Huntington Disease Organoids Humans Reproducibility of Results Deep Learning
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Robust Phase Unwrapping via Deep Image Prior for Quantitative Phase Imaging.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society Aug 10, 2021
Quantitative phase imaging (QPI) is an emerging label-free technique that produces images containing morphological and dynamical information without contrast agents. Unfortunately, the phase is wrapped in most imaging system. Phase unwrapping is the ...
Microscopy Intestine, Small Holography Tissue Culture Techniques Organoids Animals Deep Learning Image Processing, Computer-Assisted Mice Algorithms Cells, Cultured
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Artificial intelligence guided discovery of a barrier-protective therapy in inflammatory bowel disease.

Nature communications Jul 12, 2021
Modeling human diseases as networks simplify complex multi-cellular processes, helps understand patterns in noisy data that humans cannot find, and thereby improves precision in prediction. Using Inflammatory Bowel Disease (IBD) as an example, here w...
Molecular Targeted Therapy Likelihood Functions Dextran Sulfate Colitis Mice, Knockout Reproducibility of Results AMP-Activated Protein Kinases Animals Multigene Family Cohort Studies Humans Gene Expression Regulation Mice Organoids Artificial Intelligence Treatment Outcome Machine Learning Disease Models, Animal Inflammatory Bowel Diseases Mice, Inbred C57BL Intestinal Mucosa
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A deep learning model for detection and tracking in high-throughput images of organoid.

Computers in biology and medicine May 25, 2021
Organoid, an in vitro 3D culture, has extremely high similarity with its source organ or tissue, which creates a model in vitro that simulates the in vivo environment. Organoids have been extensively studied in cell biology, precision medicine, drug ...
Neural Networks, Computer Precision Medicine Deep Learning Organoids
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Rapid 3D phenotypic analysis of neurons and organoids using data-driven cell segmentation-free machine learning.

PLoS computational biology Feb 22, 2021
Phenotypic profiling of large three-dimensional microscopy data sets has not been widely adopted due to the challenges posed by cell segmentation and feature selection. The computational demands of automated processing further limit analysis of hard-...
Imaging, Three-Dimensional Image Processing, Computer-Assisted Mice Apoptosis Algorithms Phenotype Brain Animals Neurons Programming Languages Mammary Glands, Human Organoids Mice, Inbred C57BL Cell Line Autophagy Microscopy, Fluorescence Humans Machine Learning Software
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Super resolution microscopy and deep learning identify Zika virus reorganization of the endoplasmic reticulum.

Scientific reports Dec 1, 2020
The endoplasmic reticulum (ER) is a complex subcellular organelle composed of diverse structures such as tubules, sheets and tubular matrices. Flaviviruses such as Zika virus (ZIKV) induce reorganization of ER membranes to facilitate viral replicatio...
RNA, Double-Stranded Cell Line, Tumor Microscopy Extracellular Matrix Humans Zika Virus Brain Zika Virus Infection Deep Learning Viral Nonstructural Proteins Organoids Endoplasmic Reticulum
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Network-based machine learning in colorectal and bladder organoid models predicts anti-cancer drug efficacy in patients.

Nature communications Oct 30, 2020
Cancer patient classification using predictive biomarkers for anti-cancer drug responses is essential for improving therapeutic outcomes. However, current machine-learning-based predictions of drug response often fail to identify robust translational...
Biomarkers, Tumor Antineoplastic Agents Transcriptome Cell Line, Tumor Protein Interaction Maps Organoids Humans Gene Regulatory Networks Urinary Bladder Neoplasms Machine Learning Gene Expression Regulation, Neoplastic Cisplatin Colorectal Neoplasms Drug Development Fluorouracil Urinary Bladder
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OrganoidTracker: Efficient cell tracking using machine learning and manual error correction.

PloS one Oct 22, 2020
Time-lapse microscopy is routinely used to follow cells within organoids, allowing direct study of division and differentiation patterns. There is an increasing interest in cell tracking in organoids, which makes it possible to study their growth and...
Organoids Humans Neural Networks, Computer Machine Learning Software Algorithms Automation Cell Tracking
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Review of Artificial Intelligence Applications and Algorithms for Brain Organoid Research.

Interdisciplinary sciences, computational life sciences Aug 24, 2020
The human brain organoid is a miniature three-dimensional tissue culture that can simulate the structure and function of the brain in an in vitro culture environment. Although we consider that human brain organoids could be used to understand brain d...
Organoids Humans Artificial Intelligence Algorithms Brain
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CytoCensus, mapping cell identity and division in tissues and organs using machine learning.

eLife May 19, 2020
A major challenge in cell and developmental biology is the automated identification and quantitation of cells in complex multilayered tissues. We developed CytoCensus: an easily deployed implementation of supervised machine learning that extends conv...
Mutation Retina Zebrafish Machine Learning Embryo, Mammalian Female Tissue Culture Techniques Phenotype Larva Reproducibility of Results Time-Lapse Imaging Brain Animals, Genetically Modified Time Factors Microscopy, Video Animals Automation Image Processing, Computer-Assisted Organoids Male Drosophila melanogaster Mice Cell Division
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