9 results on '"Mariya Barch"'
Search Results
2. Assessing microscope image focus quality with deep learning
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Samuel J. Yang, Marc Berndl, D. Michael Ando, Mariya Barch, Arunachalam Narayanaswamy, Eric Christiansen, Stephan Hoyer, Chris Roat, Jane Hung, Curtis T. Rueden, Asim Shankar, Steven Finkbeiner, and Philip Nelson
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Image analysis ,Deep learning ,Machine learning ,Focus ,Defocus ,Image quality ,Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background Large image datasets acquired on automated microscopes typically have some fraction of low quality, out-of-focus images, despite the use of hardware autofocus systems. Identification of these images using automated image analysis with high accuracy is important for obtaining a clean, unbiased image dataset. Complicating this task is the fact that image focus quality is only well-defined in foreground regions of images, and as a result, most previous approaches only enable a computation of the relative difference in quality between two or more images, rather than an absolute measure of quality. Results We present a deep neural network model capable of predicting an absolute measure of image focus on a single image in isolation, without any user-specified parameters. The model operates at the image-patch level, and also outputs a measure of prediction certainty, enabling interpretable predictions. The model was trained on only 384 in-focus Hoechst (nuclei) stain images of U2OS cells, which were synthetically defocused to one of 11 absolute defocus levels during training. The trained model can generalize on previously unseen real Hoechst stain images, identifying the absolute image focus to within one defocus level (approximately 3 pixel blur diameter difference) with 95% accuracy. On a simpler binary in/out-of-focus classification task, the trained model outperforms previous approaches on both Hoechst and Phalloidin (actin) stain images (F-scores of 0.89 and 0.86, respectively over 0.84 and 0.83), despite only having been presented Hoechst stain images during training. Lastly, we observe qualitatively that the model generalizes to two additional stains, Hoechst and Tubulin, of an unseen cell type (Human MCF-7) acquired on a different instrument. Conclusions Our deep neural network enables classification of out-of-focus microscope images with both higher accuracy and greater precision than previous approaches via interpretable patch-level focus and certainty predictions. The use of synthetically defocused images precludes the need for a manually annotated training dataset. The model also generalizes to different image and cell types. The framework for model training and image prediction is available as a free software library and the pre-trained model is available for immediate use in Fiji (ImageJ) and CellProfiler.
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- 2018
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3. Molecular imaging with engineered physiology
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Mitul Desai, Adrian L. Slusarczyk, Ashley Chapin, Mariya Barch, and Alan Jasanoff
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Science - Abstract
The vasculature produces strong endogenous contrast in magnetic resonance imaging (MRI). Here Desai et al. report genetically encoded imaging probes derived from the vasodilator, calcitonin gene-related peptide, which allows visualization of molecular events via haemodynamic changes in optical imaging or MRI.
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- 2016
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4. Single cell tracking based on Voronoi partition via stable matching.
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Young Hwan Chang, Jeremy Linsley, Josh Lamstein, Jaslin Kalra, Irina Epstein, Mariya Barch, Kenneth Daily, Phil Snyder, Larsson Omberg, Laura Heiser, and Steven Finkbeiner
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- 2020
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5. Exceedingly small iron oxide nanoparticles as positive MRI contrast agents
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Harald Ittrich, Satoshi Okada, Ou Chen, Michael G. Kaul, Nan Li, Markus Heine, Peter Nielsen, Agata Wiśniowska, Oliver T. Bruns, Moungi G. Bawendi, Christian T. Farrar, Alan Jasanoff, Daniel M. Montana, Gerhard Adam, E. V. Hansen, Jose M. Cordero, He Wei, Yue Chen, and Mariya Barch
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Gadolinium DTPA ,Superparamagnetic iron oxide nanoparticles ,media_common.quotation_subject ,Gadolinium ,Contrast Media ,chemistry.chemical_element ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Magnetic resonance angiography ,Mice ,chemistry.chemical_compound ,Albumins ,Medical imaging ,Animals ,Humans ,Contrast (vision) ,Medicine ,Tissue Distribution ,Particle Size ,Magnetite Nanoparticles ,media_common ,Multidisciplinary ,medicine.diagnostic_test ,business.industry ,Magnetic resonance imaging ,Biological Sciences ,021001 nanoscience & nanotechnology ,medicine.disease ,Magnetic Resonance Imaging ,Ferrosoferric Oxide ,0104 chemical sciences ,chemistry ,Nephrogenic systemic fibrosis ,0210 nano-technology ,business ,Nuclear medicine ,Iron oxide nanoparticles ,Oleic Acid - Abstract
Medical imaging is routine in the diagnosis and staging of a wide range of medical conditions. In particular, magnetic resonance imaging (MRI) is critical for visualizing soft tissue and organs, with over 60 million MRI procedures performed each year worldwide. About one-third of these procedures are contrast-enhanced MRI, and gadolinium-based contrast agents (GBCAs) are the mainstream MRI contrast agents used in the clinic. GBCAs have shown efficacy and are safe to use with most patients; however, some GBCAs have a small risk of adverse effects, including nephrogenic systemic fibrosis (NSF), the untreatable condition recently linked to gadolinium (Gd) exposure during MRI with contrast. In addition, Gd deposition in the human brain has been reported following contrast, and this is now under investigation by the US Food and Drug Administration (FDA). To address a perceived need for a Gd-free contrast agent with pharmacokinetic and imaging properties comparable to GBCAs, we have designed and developed zwitterion-coated exceedingly small superparamagnetic iron oxide nanoparticles (ZES-SPIONs) consisting of ∼3-nm inorganic cores and ∼1-nm ultrathin hydrophilic shell. These ZES-SPIONs are free of Gd and show a high T1 contrast power. We demonstrate the potential of ZES-SPIONs in preclinical MRI and magnetic resonance angiography.
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- 2017
6. Screen-Based Analysis of Magnetic Nanoparticle Libraries Formed Using Peptidic Iron Oxide Ligands
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Mariya Barch, Alan Jasanoff, Satoshi Okada, and Benjamin B. Bartelle
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Phage display ,Carboxylic acid ,Iron oxide ,Contrast Media ,Nanoparticle ,02 engineering and technology ,Ligands ,010402 general chemistry ,Ferric Compounds ,01 natural sciences ,Biochemistry ,Catalysis ,Mice ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,Peptide Library ,Side chain ,Animals ,Magnetite Nanoparticles ,Peptide library ,chemistry.chemical_classification ,Communication ,General Chemistry ,021001 nanoscience & nanotechnology ,Magnetic Resonance Imaging ,Combinatorial chemistry ,Dihydroxyphenylalanine ,Molecular Imaging ,0104 chemical sciences ,chemistry ,Peptides ,0210 nano-technology ,Sequence motif ,Iron oxide nanoparticles - Abstract
The identification of effective polypeptide ligands for magnetic iron oxide nanoparticles (IONPs) could considerably accelerate the high-throughput analysis of IONP-based reagents for imaging and cell labeling. We developed a procedure for screening IONP ligands and applied it to compare candidate peptides that incorporated carboxylic acid side chains, catechols, and sequences derived from phage display selection. We found that only l-3,4-dihydroxyphenylalanine (DOPA)-containing peptides were sufficient to maintain particles in solution. We used a DOPA-containing sequence motif as the starting point for generation of a further library of over 30 peptides, each of which was complexed with IONPs and evaluated for colloidal stability and magnetic resonance imaging (MRI) contrast properties. Optimal properties were conferred by sequences within a narrow range of biophysical parameters, suggesting that these sequences could serve as generalizable anchors for formation of polypeptide-IONP complexes. Differences in the amino acid sequence affected T1- and T2-weighted MRI contrast without substantially altering particle size, indicating that the microstructure of peptide-based IONP coatings exerts a substantial influence and could be manipulated to tune properties of targeted or responsive contrast agents. A representative peptide-IONP complex displayed stability in biological buffer and induced persistent MRI contrast in mice, indicating suitability of these species for in vivo molecular imaging applications.
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- 2014
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7. Molecular imaging with engineered physiology
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Ashley A. Chapin, Alan Jasanoff, Mariya Barch, Mitul Desai, Adrian L. Slusarczyk, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology. Department of Nuclear Science and Engineering, Desai, Mitul, Slusarczyk, Adrian Lukas, Chapin, Ashley A., Barch, Mariya, and Jasanoff, Alan Pradip
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Male ,0301 basic medicine ,Science ,Calcitonin Gene-Related Peptide ,Sensitive analysis ,General Physics and Astronomy ,Physiology ,Neuroimaging ,Article ,General Biochemistry, Genetics and Molecular Biology ,Rats, Sprague-Dawley ,03 medical and health sciences ,0302 clinical medicine ,Deep tissue ,medicine ,Animals ,Humans ,Multidisciplinary ,medicine.diagnostic_test ,Chemistry ,Magnetic resonance imaging ,General Chemistry ,Rat brain ,Magnetic Resonance Imaging ,Molecular Imaging ,Rats ,3. Good health ,Oxygen ,Sprague dawley ,HEK293 Cells ,030104 developmental biology ,sense organs ,Cell tracking ,Molecular imaging ,030217 neurology & neurosurgery ,Preclinical imaging - Abstract
In vivo imaging techniques are powerful tools for evaluating biological systems. Relating image signals to precise molecular phenomena can be challenging, however, due to limitations of the existing optical, magnetic and radioactive imaging probe mechanisms. Here we demonstrate a concept for molecular imaging which bypasses the need for conventional imaging agents by perturbing the endogenous multimodal contrast provided by the vasculature. Variants of the calcitonin gene-related peptide artificially activate vasodilation pathways in rat brain and induce contrast changes that are readily measured by optical and magnetic resonance imaging. CGRP-based agents induce effects at nanomolar concentrations in deep tissue and can be engineered into switchable analyte-dependent forms and genetically encoded reporters suitable for molecular imaging or cell tracking. Such artificially engineered physiological changes, therefore, provide a highly versatile means for sensitive analysis of molecular events in living organisms., National Institute of Mental Health (U.S.) (R01-MH103160), National Institute of Mental Health (U.S.) (R01-NS076462), BRAIN Initiative (award R24-MH109081), Massachusetts Institute of Technology. Simons Center for the Social Brain, Boehringer Ingelheim Fonds (predoctoral fellowships), McGovern Institute for Brain Research at MIT
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- 2016
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8. Magneto-fluorescent core-shell supernanoparticles
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Dai Fukumura, Christian T. Farrar, Oliver T. Bruns, Jing Zhao, Mathieu Coppey, Rakesh K. Jain, He Wei, Fred Etoc, Maxime Dahan, Moungi G. Bawendi, Lars Riedemann, Peng Guo, Daniel K. Harris, Russ Jensen, Mariya Barch, Yue Chen, Jose M. Cordero, Rudolph Reimer, Hendrik Herrmann, Ou Chen, Zhongwu Wang, Jian Cui, Alan Jasanoff, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology. Department of Chemistry, Massachusetts Institute of Technology. Department of Nuclear Science and Engineering, Chen, Ou, Barch, Mariya, Zhao, Jing, Bruns, Oliver Thomas, Wei, He, Cui, Jian, Jensen, Russ, Chen, Yue, Harris, Daniel K., Cordero Hernandez, Jose M., Jasanoff, Alan Pradip, and Bawendi, Moungi G.
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Materials science ,Fluorophore ,Silicon dioxide ,Shell (structure) ,General Physics and Astronomy ,Nanoparticle ,Nanotechnology ,7. Clean energy ,General Biochemistry, Genetics and Molecular Biology ,Fluorescence ,Article ,Nanomaterials ,chemistry.chemical_compound ,Quantum Dots ,Magnetite Nanoparticles ,Fluorescent Dyes ,Multidisciplinary ,General Chemistry ,equipment and supplies ,Silicon Dioxide ,Magnetic Resonance Imaging ,3. Good health ,chemistry ,Quantum dot ,Magnetic nanoparticles - Abstract
Magneto-fluorescent particles have been recognized as an emerging class of materials that exhibit great potential in advanced applications. However, synthesizing such magneto-fluorescent nanomaterials that simultaneously exhibit uniform and tunable sizes, high magnetic content loading, maximized fluorophore coverage at the surface and a versatile surface functionality has proven challenging. Here we report a simple approach for co-assembling magnetic nanoparticles with fluorescent quantum dots to form colloidal magneto-fluorescent supernanoparticles. Importantly, these supernanoparticles exhibit a superstructure consisting of a close-packed magnetic nanoparticle ‘core’, which is fully surrounded by a ‘shell’ of fluorescent quantum dots. A thin layer of silica coating provides high colloidal stability and biocompatibility, and a versatile surface functionality. We demonstrate that after surface pegylation, these silica-coated magneto-fluorescent supernanoparticles can be magnetically manipulated inside living cells while being optically tracked. Moreover, our silica-coated magneto-fluorescent supernanoparticles can also serve as an in vivo multi-photon and magnetic resonance dual-modal imaging probe., National Institutes of Health (U.S.) (5-U54-CA151884), National Institutes of Health (U.S.) (R01-CA126642), Massachusetts Institute of Technology. Institute for Soldier Nanotechnologies (W911NF-13-D-0001)), United States. Dept. of Energy (DE-FG02-07ER46454), National Institutes of Health (U.S.) (Massachusetts Institute of Technology. Laser Biomedical Research Center 9-P41-EB015871-26A1), United States. Dept. of Energy. Office of Basic Energy Sciences (Award DE-SC0001088), United States. Dept. of Defense (Breast Cancer Research Innovator Award W81XWH-10-1-0016)), Human Frontier Science Program (Strasbourg, France) (Grant RGP0005/2007), National Institutes of Health (U.S.) (R01-DA028299), National Institutes of Health (U.S.) (R01-NS076462), European Molecular Biology Organization (Long-term Fellowship)
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- 2014
9. Detecting Force-Induced Molecular Transitions with Fluorescence Resonant Energy Transfer
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Peter B. Tarsa, Ricardo R. Brau, Mariya Barch, Jorge M. Ferrer, Yelena Freyzon, Paul Matsudaira, and Matthew J. Lang
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General Medicine - Published
- 2007
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