JoVE Journal
Biology
Biology
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Chapters
Summary
Video bioinformatics is the automated processing, analysis, understanding, and data mining of biological spatio-temporal data extracted from microscopic videos. The purpose of this article is to demonstrate a method for measuring human embryonic stem cell colony growth using a video bioinformatics method.
Tags
Video Bioinformatics Human Embryonic Stem Cells Colony Growth Video Analysis Computer Software Spatio-temporal Data Time-lapse Videos Nikon BioStation CT Camera For Video Imaging CL-Quant Software Colony Segmentation Image Enhancement Pixel Measurement Growth Rate Analysis Adobe Photoshop Software
PLAYLIST
Molecular biology toolkit
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Education • BiochemistryPhotometric Protein Determination -
Education • Basic Methods in Cellular and Molecular BiologySeparating Protein with SDS-PAGE -
Education • Basic Methods in Cellular and Molecular BiologyThe Western Blot -
Education • Basic Methods in Cellular and Molecular BiologyThe ELISA Method -
Education • ImmunologyImmunoprecipitation-Based Techniques: Purification of Endogenous Proteins Using Agarose Beads -
Education • Basic Methods in Cellular and Molecular BiologyPCR: The Polymerase Chain Reaction -
Education • Basic Methods in Cellular and Molecular BiologyDNA Gel Electrophoresis -
Education • Basic Methods in Cellular and Molecular BiologyBacterial Transformation: The Heat Shock Method -
Education • Basic Methods in Cellular and Molecular BiologyPlasmid Purification
Cell biology toolkit
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Education • Cell BiologyLive Cell Imaging of Mitosis -
Education • Cell BiologyThe Transwell Migration Assay -
Education • Cell BiologyCell-surface Biotinylation Assay -
Education • Cell BiologyFM Dyes in Vesicle Recycling -
Education • Cell BiologyThe ATP Bioluminescence Assay -
Education • BiochemistryMetabolic Labeling -
Education • Cell BiologyThe TUNEL Assay -
Education • Cell BiologyAnnexin V and Propidium Iodide Labeling -
Research • BiologyViability Assays for Cells in Culture -
Education • ImmunologyAssay for Cell Death: Chromium Release Assay of Cytotoxic Ability
Basics of cell culture
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Education • Basic Methods in Cellular and Molecular BiologyPassaging Cells -
Education • Basic Methods in Cellular and Molecular BiologyUsing a Hemacytometer to Count Cells -
Research • BiologyDetermination of Mammalian Cell Counts, Cell Size and Cell Health Using the Moxi Z Mini Automated Cell Counter -
Education • Basic Methods in Cellular and Molecular BiologyAn Introduction to Transfection -
Education • NeurosciencePrimary Neuronal Cultures -
Education • NeuroscienceNeuronal Transfection Methods -
Research • Developmental BiologyCulture and Transfection of Zebrafish Primary Cells -
Research • Immunology and InfectionHighly Efficient Transfection of Primary Macrophages with In Vitro Transcribed mRNA -
Research • BiologyHigh Yield Expression of Recombinant Human Proteins with the Transient Transfection of HEK293 Cells in Suspension -
Education • Developmental BiologyEmbryonic Stem Cell Culture and Differentiation -
Education • Developmental BiologyInduced Pluripotency
Basics of animal research
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Education • Biology IIBasic Mouse Care and Maintenance -
Education • Lab Animal ResearchRodent Handling and Restraint Techniques -
Education • Lab Animal ResearchCompound Administration I -
Education • Lab Animal ResearchCompound Administration II -
Education • Lab Animal ResearchCompound Administration III -
Education • Lab Animal ResearchCompound Administration IV -
Research • BiologyManual Restraint and Common Compound Administration Routes in Mice and Rats -
Education • Biology IIIntroducing Experimental Agents into the Mouse -
Research • BehaviorSystematic Assessment of Well-Being in Mice for Procedures Using General Anesthesia -
Education • Lab Animal ResearchBlood Withdrawal I -
Education • Lab Animal ResearchBlood Withdrawal II -
Education • Lab Animal ResearchAnesthesia Induction and Maintenance -
Education • Lab Animal ResearchConsiderations for Rodent Surgery -
Research • NeuroscienceWhole Animal Perfusion Fixation for Rodents -
Education • Lab Animal ResearchDiagnostic Necropsy and Tissue Harvest
Techniques in microscopy
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Education • General Laboratory TechniquesIntroduction to Light Microscopy -
Research • BiologyPhase Contrast and Differential Interference Contrast (DIC) Microscopy -
Education • General Laboratory TechniquesIntroduction to Fluorescence Microscopy -
Education • Analytical ChemistryScanning Electron Microscopy (SEM) -
Research • BiochemistryImaging of Extracellular Vesicles by Atomic Force Microscopy -
Education • ImmunologyConfocal Fluorescence Microscopy: A Technique to Determine the Localization of Proteins in Mouse Fibroblasts -
Research • BioengineeringVideo-rate Scanning Confocal Microscopy and Microendoscopy -
Research • BiologyThe CryoAPEX Method for Electron Microscopy Analysis of Membrane Protein Localization Within Ultrastructurally-Preserved Cells
Techniques in tissue/cell staining
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Education • General Laboratory TechniquesHistological Sample Preparation for Light Microscopy -
Education • NeuroscienceHistological Staining of Neural Tissue -
Research • Encyclopedia of Experiments: BiologyNile Red Staining of C. elegans: A Method to Visualize Lipid Droplets in Fixed Animals -
Research • Encyclopedia of Experiments: BiologyEthanol Fixation and DAPI Staining: A Method to Visualize DNA in C. elegans -
Research • NeurosciencePreparation of Non-human Primate Brain Tissue for Pre-embedding Immunohistochemistry and Electron Microscopy -
Research • Encyclopedia of Experiments: BiologyEmbedding Adult Drosophila Heads in Paraffin: Preparing Tissue for Histology -
Research • BiologyCryosectioning of Contiguous Regions of a Single Mouse Skeletal Muscle for Gene Expression and Histological Analyses -
Research • MedicineSampling Strategies and Processing of Biobank Tissue Samples from Porcine Biomedical Models -
Education • ImmunologyImmunohistochemistry and Immunocytochemistry: Tissue Imaging via Light Microscopy -
Education • ImmunologyImmunofluorescence Microscopy: Immunofluorescence Staining of Paraffin-Embedded Tissue Sections -
Research • NeuroscienceImmunostaining of Biocytin-filled and Processed Sections for Neurochemical Markers -
Education • Developmental BiologyWhole-Mount In Situ Hybridization
Techniques in analytical chemistry
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Education • Core: ChemistryUncertainty in Measurement: Accuracy and Precision -
Education • Analytical ChemistryInternal Standards -
Education • Analytical ChemistryCalibration Curves -
Education • Analytical ChemistryMethod of Standard Addition -
Education • Analytical ChemistrySample Preparation for Analytical Characterization -
Education • Analytical ChemistryIntroduction to Mass Spectrometry -
Education • BiochemistryTandem Mass Spectrometry -
Research • BioengineeringSample Preparation Strategies for Mass Spectrometry Imaging of 3D Cell Culture Models -
Research • GeneticsMass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames -
Education • Materials EngineeringX-ray Diffraction -
Education • Analytical ChemistryRaman Spectroscopy for Chemical Analysis -
Education • Analytical ChemistryUltraviolet-Visible (UV-Vis) Spectroscopy -
Research • EngineeringQuasi-light Storage for Optical Data Packets -
Education • Analytical ChemistryHigh-Performance Liquid Chromatography (HPLC) -
Education • Analytical ChemistryGas Chromatography (GC) with Flame-Ionization Detection
Techniques in genotyping
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Education • Biology IIMouse Genotyping -
Education • GeneticsSNP Genotyping -
Research • BiologyRapid Genotyping of Mouse Tissue Using Sigma's Extract-N-Amp Tissue PCR Kit -
Research • BiologyInfinium Assay for Large-scale SNP Genotyping Applications -
Research • BiologyA PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica -
Research • Developmental BiologyGenotyping and Quantification of In Situ Hybridization Staining in Zebrafish -
Research • MedicineCollection and Extraction of Saliva DNA for Next Generation Sequencing -
Research • BiologyAmplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites -
Research • BiologyNext-generation Sequencing of 16S Ribosomal RNA Gene Amplicons -
Research • BiologyTargeted DNA Methylation Analysis by Next-generation Sequencing
Biostatistical analysis, bioinformatics and big data
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Education • Core: PsychologyMeasures of Central Tendency -
Education • Core: PsychologyVariation: Normal Distribution, Range, and Standard Deviation -
Education • Core: PsychologyRegression Toward the Mean -
Education • Core: PsychologyStatistical Significance -
Research • NeuroscienceStatistical Modelling of Cortical Connectivity Using Non-invasive Electroencephalograms -
Research • BiochemistryFully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules -
Research • BehaviorAutomated, Quantitative Cognitive/Behavioral Screening of Mice: For Genetics, Pharmacology, Animal Cognition and Undergraduate Instruction -
Research • Cancer ResearchIntegration of Bioinformatics Approaches and Experimental Validations to Understand the Role of Notch Signaling in Ovarian Cancer -
Research • BiologyVideo Bioinformatics Analysis of Human Embryonic Stem Cell Colony Growth -
Research • GeneticsTargeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease -
Research • GeneticsRNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level -
Research • GeneticsA Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants -
Research • BiologyA Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
