AIMC Topic: Embryo, Nonmammalian
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FlyIT: Drosophila Embryogenesis Image Annotation based on Image Tiling and Convolutional Neural Networks.
IEEE/ACM transactions on computational biology and bioinformatics
Feb 3, 2021
With the rise of image-based transcriptomics, spatial gene expression data has become increasingly important for understanding gene regulations from the tissue level down to the cell level. Especially, the gene expression images of Drosophila embryos...
A deep learning approach for staging embryonic tissue isolates with small data.
PloS one
Jan 8, 2021
Machine learning approaches are becoming increasingly widespread and are now present in most areas of research. Their recent surge can be explained in part due to our ability to generate and store enormous amounts of data with which to train these mo...
Establishment of a morphological atlas of the Caenorhabditis elegans embryo using deep-learning-based 4D segmentation.
Nature communications
Dec 7, 2020
The invariant development and transparent body of the nematode Caenorhabditis elegans enables complete delineation of cell lineages throughout development. Despite extensive studies of cell division, cell migration and cell fate differentiation, cell...
Deep learning enables automated volumetric assessments of cardiac function in zebrafish.
Disease models & mechanisms
Oct 25, 2019
Although the zebrafish embryo is a powerful animal model of human heart failure, the methods routinely employed to monitor cardiac function produce rough approximations that are susceptible to bias and inaccuracies. We developed and validated a deep ...
Trace, Machine Learning of Signal Images for Trace-Sensitive Mass Spectrometry: A Case Study from Single-Cell Metabolomics.
Analytical chemistry
Apr 15, 2019
Recent developments in high-resolution mass spectrometry (HRMS) technology enabled ultrasensitive detection of proteins, peptides, and metabolites in limited amounts of samples, even single cells. However, extraction of trace-abundance signals from c...
Zebrafish Embryo Vessel Segmentation Using a Novel Dual ResUNet Model.
Computational intelligence and neuroscience
Feb 3, 2019
Zebrafish embryo fluorescent vessel analysis, which aims to automatically investigate the pathogenesis of diseases, has attracted much attention in medical imaging. Zebrafish vessel segmentation is a fairly challenging task, which requires distinguis...
Deep learning image recognition enables efficient genome editing in zebrafish by automated injections.
PloS one
Jan 7, 2019
One of the most popular techniques in zebrafish research is microinjection. This is a rapid and efficient way to genetically manipulate early developing embryos, and to introduce microbes, chemical compounds, nanoparticles or tracers at larval stages...
High throughput automated detection of axial malformations in Medaka embryo.
Computers in biology and medicine
Jan 3, 2019
Fish embryo models are widely used as screening tools to assess the efficacy and/or toxicity of chemicals. This assessment involves the analysis of embryo morphological abnormalities. In this article, we propose a multi-scale pipeline to allow automa...
Acquisition and reconstruction of 4D surfaces of axolotl embryos with the flipping stage robotic microscope.
Bio Systems
Oct 25, 2018
We have designed and constructed a Flipping Stage for a light microscope that can view the whole exterior surface of a 2 mm diameter developing axolotl salamander embryo. It works by rapidly inverting the bottom-heavy embryo, imaging it as it rights ...
(Machine-)Learning to analyze in vivo microscopy: Support vector machines.
Biochimica et biophysica acta. Proteins and proteomics
Sep 30, 2017
The development of new microscopy techniques for super-resolved, long-term monitoring of cellular and subcellular dynamics in living organisms is revealing new fundamental aspects of tissue development and repair. However, new microscopy approaches p...
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