Automatic Segmentation of Neurons from Fluorescent Microscopy Imaging

2018 ◽  
pp. 121-133
Author(s):  
Silvia Baglietto ◽  
Ibolya E. Kepiro ◽  
Gerrit Hilgen ◽  
Evelyne Sernagor ◽  
Vittorio Murino ◽  
...  
Keyword(s):  
Automatic Segmentation ◽  
Fluorescent Microscopy ◽  
Microscopy Imaging

scholarly journals Cytokit: a single-cell analysis toolkit for high dimensional fluorescent microscopy imaging

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Eric Czech ◽  
Bulent Arman Aksoy ◽  
Pinar Aksoy ◽  
Jeff Hammerbacher
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Fluorescent Microscopy ◽  
High Dimensional ◽  
Cell Analysis ◽  
Microscopy Imaging

scholarly journals PDTM-30. UNDERSTANDING THE EFFECTS OF MOLECULAR SIZE ON VOLUME OF DISTRIBUTION IN CONVECTION-ENHANCED DELIVERY

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi193-vi194
Author(s):  
Erica Power ◽  
Julian Rechberger ◽  
Liang Zhang ◽  
David Daniels
Keyword(s):  
Molecular Weight ◽  
Single Injection ◽  
Fluorescent Microscopy ◽  
Molecular Size ◽  
Volume Of Distribution ◽  
Sprague Dawley ◽  
Convection Enhanced Delivery ◽  
Microscopy Imaging ◽  
Delivery Technique ◽  
The Brain

Abstract BACKGROUND Diffuse midline gliomas harboring the H3K27M mutation, previously known as diffuse intrinsic pontine gliomas (DIPG), are rare and aggressive pediatric brain tumors. Over 100 clinical trials with different chemotherapeutics have failed to show any therapeutic benefit. One reason for failure is likely due to poor delivery of these agents to the brainstem. Convection-enhanced delivery (CED) is an emerging delivery technique used to directly inject the agent of interest into the brainstem under pressure. While there is evidence that this may be an effective delivery method, little work has been done to understand the optimal physical properties of these drugs. We sought characterize volume of distribution in the brain based on molecular size of the agent delivered via CED. METHODS Sprague- Dawley rats underwent a single injection of FITC-dextran (3,000 Da, 10,000 Da, 20,000 Da, 70,000 Da, 150,000 Da) via CED into the pons. Post-injection, animals were sacrificed and their brains harvested. Fluorescent microscopy imaging was used to calculate the volume of distribution of the FITC-dextran throughout the brain. RESULTS The volume of distribution (Vd) decreased exponentially according to a two-phase delay (r2= 0.94) as the molecular size of the FITC-dextran increased. The highest mean Vd (107.87mm3) was at a molecular weight of 3,000 Da, and lowest mean Vd (26.48 mm3) was at a molecular weight of 150,000 Da. ANOVA analysis was statistically significant (p= 0.0017). CONCLUSIONS As the molecular size of the FITC-dextran increased, the volume of distribution within the brain following a single injection via CED into the pons decreased. A better understanding of how drugs distribute by convection will allow us to optimize treatment regimens for DIPG tumors.

Design and Development of Light-Sensitive Chitosan-Based Nanocarriers for Gene Delivery

2012 ◽  
Vol 86 ◽  
pp. 75-80 ◽  
Author(s):  
Nicolas Duceppe ◽  
Maryam Tabrizian
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Uv Light ◽  
Transfection Efficiency ◽  
Fluorescent Microscopy ◽  
Amide Bond ◽  
Microscopy Imaging ◽  
Hek 293 ◽  
Dna Release ◽  
Nuclear Magnetic

In this work, we report on the development of a multifunctional and photo-inducible nanoplex made of chitosan (Ch) and hyaluronic acid (HA) for delivery of nucleic acid. Self-assembled Ch/HA nanoparticles were attached to ortho-nitrobenzyl (o-NB) photo-labile molecules (PL)-gold nanoparticles via thiol groups and to QDs-conjugate ssDNA through amide bond linkage to form nanoplexes (Ch:HA:AuPL:QD-DNA). The composition of DNA nanocarriers was validated by nuclear magnetic resonance, transmission electronic microscopy, energy dispersive x-ray spectroscopy, gel electrophoresis and spectrophotometry. The change in zeta potential (34 ± 11 to -26 ± 11 mV) and the loss of the o-NB characteristic peaks in nuclear magnetic resonance spectra, after the exposure of the PL molecule to ultraviolet light, both confirmed the photo-labile properties of the system. The potential of the nanoplexes to induce high cell transfection was assessed by flow cytometry and fluorescent microscopy imaging. Over 30% transfection of HEK-293 was obtained with the nanoplexes after a one-minute exposure of cells to UV light. This corresponds to a 15% increase in the transfection efficiency compared to unexposed Ch:HA:AuPL:QD-DNA nanocarriers. This high transfection efficiency was associated with the unique design of the carrier system and its photo-responsiveness feature for facilitating the DNA release.

scholarly journals Novel Infectivity-Enhanced Oncolytic Adenovirus with a Capsid-Incorporated Dual-Imaging Moiety for Monitoring Virotherapy in Ovarian Cancer

2009 ◽  
Vol 8 (5) ◽  
pp. 7290.2009.00025 ◽  
Author(s):  
Kristopher J. Kimball ◽  
Angel A. Rivera ◽  
Kurt R. Zinn ◽  
Mert Icyuz ◽  
Vaibhav Saini ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Cancer Cells ◽  
Fluorescent Protein ◽  
Imaging Modality ◽  
Fluorescent Microscopy ◽  
Oncolytic Adenovirus ◽  
Ovarian Cancer Cells ◽  
Microscopy Imaging ◽  
Dual Imaging

We sought to develop a cancer-targeted, infectivity-enhanced oncolytic adenovirus that embodies a capsid-labeling fusion for non-invasive dual-modality imaging of ovarian cancer virotherapy. A functional fusion protein composed of fluorescent and nuclear imaging tags was genetically incorporated into the capsid of an infectivity-enhanced conditionally replicative adenovirus. Incorporation of herpes simplex virus thymidine kinase (HSV-tk) and monomeric red fluorescent protein 1 (mRFP1) into the viral capsid and its genomic stability were verified by molecular analyses. Replication and oncolysis were evaluated in ovarian cancer cells. Fusion functionality was confirmed by in vitro gamma camera and fluorescent microscopy imaging. Comparison of tk-mRFP virus to single-modality controls revealed similar replication efficiency and oncolytic potency. Molecular fusion did not abolish enzymatic activity of HSV-tk as the virus effectively phosphorylated thymidine both ex vivo and in vitro. In vitro fluorescence imaging demonstrated a strong correlation between the intensity of fluorescent signal and cytopathic effect in infected ovarian cancer cells, suggesting that fluorescence can be used to monitor viral replication. We have in vitro validated a new infectivity-enhanced oncolytic adenovirus with a dual-imaging modality-labeled capsid, optimized for ovarian cancer virotherapy. The new agent could provide incremental gains toward climbing the barriers for achieving conditionally replicated adenovirus efficacy in human trials.

scholarly journals Short OGA is targeted to the mitochondria and regulates mitochondrial reactive oxygen species level

2021 ◽  
Author(s):  
Patrick Pagesy ◽  
Abdelouhab Bouaboud ◽  
Zhihao Feng ◽  
Philippe Hulin ◽  
Tarik Issad
Keyword(s):  
Splice Variants ◽  
Fluorescent Microscopy ◽  
Cell Fractionation ◽  
Oxygen Species ◽  
Mitochondrial Reactive Oxygen Species ◽  
Post Translational Modification ◽  
Mouse Embryonic Fibroblasts ◽  
Embryonic Fibroblasts ◽  
Microscopy Imaging ◽  
Mitochondrial Ros

O-GlcNAcylation is a reversible post-translational modification involved the regulation of cytosolic, nuclear and mitochondrial proteins. Only two enzymes, OGT and OGA, control attachment and removal of O-GlcNAc on proteins, respectively. Whereas a variant OGT (mOGT) has been proposed as the main isoform that O-GlcNAcylates proteins in mitochondria, identification of a mitochondrial OGA has not been performed yet. Two splice variants of OGA (short and long isoforms) have been described previously. In this work, using cell fractionation experiments, we show that short-OGA is preferentially recovered in mitochondria-enriched fractions from HEK-293T cells as well as mouse embryonic fibroblasts. Moreover, fluorescent microscopy imaging confirmed that GFP-tagged short-OGA is addressed to mitochondria. In addition, using a BRET-based mitochondrial O-GlcNAcylation biosensor, we show that co-transfection of short-OGA markedly reduced O-GlcNAcylation of the biosensor, whereas long-OGA had no significant effect. Finally, using genetically encoded or chemical fluorescent mitochondrial probes, we showed that short-OGA overexpression increases mitochondrial ROS levels, whereas long-OGA had no significant effect. Together, our work reveals that the short-OGA isoform is targeted to the mitochondria where it regulates ROS homoeostasis.

scholarly journals Automatic Segmentation and Cardiac Mechanics Analysis of Evolving Zebrafish Using Deep Learning

2021 ◽  
Vol 8 ◽  
Author(s):  
Bohan Zhang ◽  
Kristofor E. Pas ◽  
Toluwani Ijaseun ◽  
Hung Cao ◽  
Peng Fei ◽  
...  
Keyword(s):  
Deep Learning ◽  
Cardiac Development ◽  
Imaging Techniques ◽  
Automatic Segmentation ◽  
Fluorescent Microscopy ◽  
Cardiac Mechanics ◽  
Light Sheet ◽  
Training Data ◽  
Volume Changes ◽  
Biomedical Analysis

Background: In the study of early cardiac development, it is essential to acquire accurate volume changes of the heart chambers. Although advanced imaging techniques, such as light-sheet fluorescent microscopy (LSFM), provide an accurate procedure for analyzing the heart structure, rapid, and robust segmentation is required to reduce laborious time and accurately quantify developmental cardiac mechanics.Methods: The traditional biomedical analysis involving segmentation of the intracardiac volume occurs manually, presenting bottlenecks due to enormous data volume at high axial resolution. Our advanced deep-learning techniques provide a robust method to segment the volume within a few minutes. Our U-net-based segmentation adopted manually segmented intracardiac volume changes as training data and automatically produced the other LSFM zebrafish cardiac motion images.Results: Three cardiac cycles from 2 to 5 days postfertilization (dpf) were successfully segmented by our U-net-based network providing volume changes over time. In addition to understanding each of the two chambers' cardiac function, the ventricle and atrium were separated by 3D erode morphology methods. Therefore, cardiac mechanical properties were measured rapidly and demonstrated incremental volume changes of both chambers separately. Interestingly, stroke volume (SV) remains similar in the atrium while that of the ventricle increases SV gradually.Conclusion: Our U-net-based segmentation provides a delicate method to segment the intricate inner volume of the zebrafish heart during development, thus providing an accurate, robust, and efficient algorithm to accelerate cardiac research by bypassing the labor-intensive task as well as improving the consistency in the results.

scholarly journals Automatic segmentation and cardiac mechanics analysis of evolving zebrafish using deep-learning

2021 ◽  
Author(s):  
Bohan Zhang ◽  
Kristofor Pas ◽  
Toluwani Ijaseun ◽  
Hung Cao ◽  
Peng Fei ◽  
...  
Keyword(s):  
Deep Learning ◽  
Cardiac Development ◽  
Imaging Techniques ◽  
Automatic Segmentation ◽  
Fluorescent Microscopy ◽  
Cardiac Mechanics ◽  
Light Sheet ◽  
Training Data ◽  
Volume Changes ◽  
Biomedical Analysis

AbstractObjectiveIn the study of early cardiac development, it is important to acquire accurate volume changes of the heart chambers. Although advanced imaging techniques, such as light-sheet fluorescent microscopy (LSFM), provide an accurate procedure for analyzing the structure of the heart, rapid and robust segmentation is required to reduce laborious time and accurately quantify developmental cardiac mechanics.MethodsThe traditional biomedical analysis involving segmentation of the intracardiac volume is usually carried out manually, presenting bottlenecks due to enormous data volume at high axial resolution. Our advanced deep-learning techniques provide a robust method to segment the volume within a few minutes. Our U-net based segmentation adopted manually segmented intracardiac volume changes as training data and produced the other LSFM zebrafish cardiac motion images automatically.ResultsThree cardiac cycles from 2 days post fertilization (dpf) to 5 dpf were successfully segmented by our U-net based network providing volume changes over time. In addition to understanding the cardiac function for each of the two chambers, the ventricle and atrium were separated by 3D erode morphology methods. Therefore, cardiac mechanical properties were measured rapidly and demonstrated incremental volume changes of both chambers separately. Interestingly, stroke volume (SV) remains similar in the atrium while that of the ventricle increases SV gradually.ConclusionOur U-net based segmentation provides a delicate method to segment the intricate inner volume of zebrafish heart during development; thus providing an accurate, robust and efficient algorithm to accelerate cardiac research by bypassing the labor-intensive task as well as improving the consistency in the results.

scholarly journals Neural Selective Cryoneurolysis with Ice Slurry Injection in a Rat Model

2020 ◽  
Vol 133 (1) ◽  
pp. 185-194 ◽  
Author(s):  
Lilit Garibyan ◽  
Sara Moradi Tuchayi ◽  
Ying Wang ◽  
Alla Khodorova ◽  
Anat Stemmer-Rachamimov ◽  
...  
Keyword(s):  
Postoperative Pain ◽  
Sciatic Nerve ◽  
Fluorescent Microscopy ◽  
Surrounding Tissue ◽  
Nociceptive Response ◽  
Ice Slurry ◽  
Microscopy Imaging ◽  
Selective Method ◽  
Rat Sciatic Nerve ◽  
Slurry Injection

Background Postoperative pain caused by trauma to nerves and tissue around the surgical site is a major problem. Perioperative steps to reduce postoperative pain include local anesthetics and opioids, the latter of which are addictive and have contributed to the opioid epidemic. Cryoneurolysis is a nonopioid and long-lasting treatment for reducing postoperative pain. However, current methods of cryoneurolysis are invasive, technically demanding, and are not tissue-selective. This project aims to determine whether ice slurry can be used as a novel, injectable, drug-free, and tissue-selective method of cryoneurolysis and resulting analgesia. Methods The authors developed an injectable and selective method of cryoneurolysis using biocompatible ice slurry, using rat sciatic nerve to investigate the effect of slurry injection on the structure and function of the nerve. Sixty-two naïve, male Sprague-Dawley rats were used in this study. Advanced Coherent anti-Stokes Raman Scattering microscopy, light, and fluorescent microscopy imaging were used at baseline and at various time points after treatment for evaluation and quantification of myelin sheath and axon structural integrity. Validated motor and sensory testing were used for evaluating the sciatic nerve function in response to ice slurry treatment. Results Ice slurry injection can selectively target the rat sciatic nerve. Being injectable, it can infiltrate around the nerve. The authors demonstrate that a single injection is safe and selective for reversibly disrupting the myelin sheaths and axon density, with complete structural recovery by day 112. This leads to decreased nocifensive function for up to 60 days, with complete recovery by day 112. There was up to median [interquartile range]: 68% [60 to 94%] reduction in mechanical pain response after treatment. Conclusions Ice slurry injection selectively targets the rat sciatic nerve, causing no damage to surrounding tissue. Injection of ice slurry around the rat sciatic nerve induced decreased nociceptive response from the baseline through neural selective cryoneurolysis. Editor’s Perspective What We Already Know about This Topic What This Article Tells Us That Is New

scholarly journals Embryonic Heart Morphogenesis from Confocal Microscopy Imaging and Automatic Segmentation

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Hongda Mao ◽  
Megan Gribble ◽  
Arkady M. Pertsov ◽  
Pengcheng Shi
Keyword(s):  
Confocal Microscopy ◽  
Penetration Depth ◽  
Spatial Resolution ◽  
Active Contour Model ◽  
Automatic Segmentation ◽  
Embryonic Heart ◽  
Imaging Method ◽  
Microscopy Imaging ◽  
Heart Morphogenesis ◽  
Confocal Microscopy Imaging

Embryonic heart morphogenesis (EHM) is a complex and dynamic process where the heart transforms from a single tube into a four-chambered pump. This process is of great biological and clinical interest but is still poorly understood for two main reasons. On the one hand, the existing imaging modalities for investigating EHM suffered from either limited penetration depth or limited spatial resolution. On the other hand, current works typically adopted manual segmentation, which was tedious, subjective, and time consuming considering the complexity of developing heart geometry and the large size of images. In this paper, we propose to utilize confocal microscopy imaging with tissue optical immersion clearing technique to image the heart at different stages of development for EHM study. The imaging method is able to produce high spatial resolution images and achieve large penetration depth at the same time. Furthermore, we propose a novel convex active contour model for automatic image segmentation. The model has the ability to deal with intensity fall-off in depth which is characterized by confocal microscopy images. We acquired the images of embryonic quail hearts from day 6 to day 14 of incubation for EHM study. The experimental results were promising and provided us with an insight view of early heart growth pattern and also paved the road for data-driven heart growth modeling.

scholarly journals Quantification and its Applications in Fluorescent Microscopy Imaging

Traffic ◽  
2009 ◽  
Vol 10 (8) ◽  
pp. 951-961 ◽  
Author(s):  
Nicholas Hamilton
Keyword(s):  
Fluorescent Microscopy ◽  
Microscopy Imaging
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