Kooperativer Bibliotheksverbund

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Format: 1 online resource (240 pages)

Edition: 1st ed.

ISBN: 9780128222102

Note: Front Cover -- Revealing Uncharted Biology With Single Cell Multiplex Proteomic Technologies -- Revealing Uncharted Biology With Single Cell Multiplex Proteomic Technologies -- Copyright -- Dedication -- Contents -- Contributors -- Foreword -- Acknowledgments -- 1 - Personal and historical recollections of the early years of mass cytometry -- The evolution of DVS Sciences -- The culture of the early mass cytometry team -- Lessons learned/advice to an entrepreneur -- A short overview of the CyTOF technology -- A short overview of the MAXPAR technology -- References -- 2 - Unveiling spatial biology of cellular landscapes with imaging mass cytometry -- Introduction to imaging mass cytometry -- Overview -- Principles of imaging mass cytometry -- How imaging mass cytometry works -- History of imaging mass cytometry -- Features of imaging mass cytometry -- Imaging mass cytometry workflow -- Multiplex antibody panel design -- Staining tissues -- Image acquisition -- Image analysis -- IMC reveals the secrets of spatial biology in tissues -- Physiology of normal tissue -- Cancer -- Breast cancer -- Colorectal cancer -- Lung cancer -- Melanoma -- Brain cancer -- Preclinical tumor studies with model organisms -- Neurodegenerative diseases -- Parkinson's disease -- Multiple sclerosis -- Inflammatory diseases -- Future of imaging mass cytometry -- Summary -- Acknowledgments -- References -- 3 - Single-cell spatial phenotype mapping of tissue microenvironments with multiplexed ion beam imaging (MIBI): A highly multiplexed, high-resolution spatial proteomic approach for tissue imaging and analysis -- Introduction -- Importance of spatial context in tissue biology -- Limitations of traditional tissue analysis -- Emergence of multiplexed tissue imaging for spatial biology -- Fundamental principles of MIBI -- MIBI leverages mass spectrometry. , MIBI analysis involves a targeted immunoassay for protein marker identifiers of cell phenotype and state -- Aspects of MIBI analysis -- The MIBI workflow -- Components of the MIBI platform -- Considerations for experimental design -- MIBI data analysis -- Applications | Unlocking unchartered biology with MIBI -- Revealing the tumor-immune microenvironment structures of triple negative breast cancer -- Revealing spatial signatures of progression from DCIS to invasive breast cancer -- Revealing signatures linked to metastasis and immunosuppression in lung cancer -- Monitoring immune response in tumor therapy development -- Spatial metabolic profiling of cytotoxic T cells in human colorectal carcinoma -- Understanding the inflammatory state of immunotherapy-driven gastritis -- Exploring the immunoregulatory landscape of tuberculosis granulomas -- Investigating the orchestrated immune events of viral persistence in retroviral infection -- Capturing human neuropathology in neurodegenerative disease -- Conclusion -- Glossary -- References -- 4 - Highly multiplexed spatial protein data using CODEX technology -- Introduction -- Fundamental principles of CODEX -- Strengths and limitations of CODEX technology -- Codex instrument -- Considerations for experimental design -- CODEX data collection -- Data analysis-Tools and tips -- Visualizing unchartered biology -- Future directions -- Glossaries -- References -- Further reading -- 5 - Exploring uncharted spatial biology with ChipCytometry highly multiplexed imaging -- Introduction -- Fundamental principles of ChipCytometry -- ChipCytometry workflow -- Methods for signal removal -- Technique strengths and limitations -- Increasing plex through cycle count -- Antibodies from any commercial vendor -- Walk-away automation -- High-throughput imaging -- Subcellular imaging -- Multiexposure HDR image fusion. , Equipment involved -- Biological materials and applications -- Fluorescent antibodies -- Imaging with CellScape -- Microfluidics unit -- CellScape microfluidic chip -- Experimental design considerations -- Antibody validation for ChipCytometry -- ChipCytometry antibody panel design -- Optimizing antigen retrieval -- Experimental data collection -- Image acquisition -- Image processing -- Cell segmentation -- Cell phenotyping -- Visualizing unchartered biology -- References -- 6 - Combined nucleic acid and protein quantification in the native tissue microenvironment -- Introduction -- Immuno-fluorescence-based multiplexed IHC -- Multiplexed IHC by rasterization and mass spectrometry -- Highly multiplexed fluorescence in situ hybridization -- Other strategies -- Combined spatial-omics -- Computational tools -- Conclusions -- Acknowledgments -- References -- 7 - Tissue schematics: Representing tissues as assemblies of neighborhoods -- Introduction -- Principles underlying tissue schematics -- Strengths and limitations -- Experimental context considerations -- Technical considerations -- Equipment involved -- Experiment design considerations -- Constructing tissue schematics -- Identifying cell types -- Identifying cellular neighborhoods -- Identifying spatial contexts -- Indexing tissue motifs -- Identifying assembly rules -- Interpreting tissue schematics -- Interpreting cellular neighborhoods -- Interpreting spatial contexts -- Interpreting assembly rules -- Uncharted biology visualized by tissue schematics -- Key terms and definitions -- References -- 8 - High-definition CODEX for 3D multiplex spatial cell phenotyping -- Introduction -- CODEX principles, strengths, and limitations -- Experimental design, equipment, and considerations -- Visualizing uncharted biology. , HD-CODEX allows for multiplexing protein targets in tissues at unprecedented resolution -- HD-CODEX provides insight into significant cell-cell spatial differences in 3D protein expression -- Advice for novice CODEX and HD-CODEX users -- Future directions -- Key terms and definitions -- Omics -- Proteomics -- Sequencing -- Phenotyping -- Clustering -- Image resolution -- Cell segmentation -- Fluorescence microscopy -- Antibody -- Reagent -- Hypothesis test -- Null hypothesis -- Uniform manifold approximation and projection -- Wilcoxon signed-rank test -- Jaccard index -- Kolmogorov-Smirnov hypothesis test -- Z-stack -- References -- Index -- Back Cover.

Additional Edition: Print version: Fantl, Wendy Revealing Uncharted Biology with Single Cell Multiplex Proteomic Technologies San Diego : Elsevier Science & Technology,c2024 ISBN 9780128222096

Language: English

UID:

Format: 1 online resource (240 pages)

Edition: 1st ed.

ISBN: 9780128222102

Note: Front Cover -- Revealing Uncharted Biology With Single Cell Multiplex Proteomic Technologies -- Revealing Uncharted Biology With Single Cell Multiplex Proteomic Technologies -- Copyright -- Dedication -- Contents -- Contributors -- Foreword -- Acknowledgments -- 1 - Personal and historical recollections of the early years of mass cytometry -- The evolution of DVS Sciences -- The culture of the early mass cytometry team -- Lessons learned/advice to an entrepreneur -- A short overview of the CyTOF technology -- A short overview of the MAXPAR technology -- References -- 2 - Unveiling spatial biology of cellular landscapes with imaging mass cytometry -- Introduction to imaging mass cytometry -- Overview -- Principles of imaging mass cytometry -- How imaging mass cytometry works -- History of imaging mass cytometry -- Features of imaging mass cytometry -- Imaging mass cytometry workflow -- Multiplex antibody panel design -- Staining tissues -- Image acquisition -- Image analysis -- IMC reveals the secrets of spatial biology in tissues -- Physiology of normal tissue -- Cancer -- Breast cancer -- Colorectal cancer -- Lung cancer -- Melanoma -- Brain cancer -- Preclinical tumor studies with model organisms -- Neurodegenerative diseases -- Parkinson's disease -- Multiple sclerosis -- Inflammatory diseases -- Future of imaging mass cytometry -- Summary -- Acknowledgments -- References -- 3 - Single-cell spatial phenotype mapping of tissue microenvironments with multiplexed ion beam imaging (MIBI): A highly multiplexed, high-resolution spatial proteomic approach for tissue imaging and analysis -- Introduction -- Importance of spatial context in tissue biology -- Limitations of traditional tissue analysis -- Emergence of multiplexed tissue imaging for spatial biology -- Fundamental principles of MIBI -- MIBI leverages mass spectrometry. , MIBI analysis involves a targeted immunoassay for protein marker identifiers of cell phenotype and state -- Aspects of MIBI analysis -- The MIBI workflow -- Components of the MIBI platform -- Considerations for experimental design -- MIBI data analysis -- Applications | Unlocking unchartered biology with MIBI -- Revealing the tumor-immune microenvironment structures of triple negative breast cancer -- Revealing spatial signatures of progression from DCIS to invasive breast cancer -- Revealing signatures linked to metastasis and immunosuppression in lung cancer -- Monitoring immune response in tumor therapy development -- Spatial metabolic profiling of cytotoxic T cells in human colorectal carcinoma -- Understanding the inflammatory state of immunotherapy-driven gastritis -- Exploring the immunoregulatory landscape of tuberculosis granulomas -- Investigating the orchestrated immune events of viral persistence in retroviral infection -- Capturing human neuropathology in neurodegenerative disease -- Conclusion -- Glossary -- References -- 4 - Highly multiplexed spatial protein data using CODEX technology -- Introduction -- Fundamental principles of CODEX -- Strengths and limitations of CODEX technology -- Codex instrument -- Considerations for experimental design -- CODEX data collection -- Data analysis-Tools and tips -- Visualizing unchartered biology -- Future directions -- Glossaries -- References -- Further reading -- 5 - Exploring uncharted spatial biology with ChipCytometry highly multiplexed imaging -- Introduction -- Fundamental principles of ChipCytometry -- ChipCytometry workflow -- Methods for signal removal -- Technique strengths and limitations -- Increasing plex through cycle count -- Antibodies from any commercial vendor -- Walk-away automation -- High-throughput imaging -- Subcellular imaging -- Multiexposure HDR image fusion. , Equipment involved -- Biological materials and applications -- Fluorescent antibodies -- Imaging with CellScape -- Microfluidics unit -- CellScape microfluidic chip -- Experimental design considerations -- Antibody validation for ChipCytometry -- ChipCytometry antibody panel design -- Optimizing antigen retrieval -- Experimental data collection -- Image acquisition -- Image processing -- Cell segmentation -- Cell phenotyping -- Visualizing unchartered biology -- References -- 6 - Combined nucleic acid and protein quantification in the native tissue microenvironment -- Introduction -- Immuno-fluorescence-based multiplexed IHC -- Multiplexed IHC by rasterization and mass spectrometry -- Highly multiplexed fluorescence in situ hybridization -- Other strategies -- Combined spatial-omics -- Computational tools -- Conclusions -- Acknowledgments -- References -- 7 - Tissue schematics: Representing tissues as assemblies of neighborhoods -- Introduction -- Principles underlying tissue schematics -- Strengths and limitations -- Experimental context considerations -- Technical considerations -- Equipment involved -- Experiment design considerations -- Constructing tissue schematics -- Identifying cell types -- Identifying cellular neighborhoods -- Identifying spatial contexts -- Indexing tissue motifs -- Identifying assembly rules -- Interpreting tissue schematics -- Interpreting cellular neighborhoods -- Interpreting spatial contexts -- Interpreting assembly rules -- Uncharted biology visualized by tissue schematics -- Key terms and definitions -- References -- 8 - High-definition CODEX for 3D multiplex spatial cell phenotyping -- Introduction -- CODEX principles, strengths, and limitations -- Experimental design, equipment, and considerations -- Visualizing uncharted biology. , HD-CODEX allows for multiplexing protein targets in tissues at unprecedented resolution -- HD-CODEX provides insight into significant cell-cell spatial differences in 3D protein expression -- Advice for novice CODEX and HD-CODEX users -- Future directions -- Key terms and definitions -- Omics -- Proteomics -- Sequencing -- Phenotyping -- Clustering -- Image resolution -- Cell segmentation -- Fluorescence microscopy -- Antibody -- Reagent -- Hypothesis test -- Null hypothesis -- Uniform manifold approximation and projection -- Wilcoxon signed-rank test -- Jaccard index -- Kolmogorov-Smirnov hypothesis test -- Z-stack -- References -- Index -- Back Cover.

Additional Edition: Print version: Fantl, Wendy Revealing Uncharted Biology with Single Cell Multiplex Proteomic Technologies San Diego : Elsevier Science & Technology,c2024 ISBN 9780128222096

Language: English

UID:

Format: 1 online resource (240 pages)

Edition: 1st ed.

ISBN: 9780128222102

Note: Front Cover -- Revealing Uncharted Biology With Single Cell Multiplex Proteomic Technologies -- Revealing Uncharted Biology With Single Cell Multiplex Proteomic Technologies -- Copyright -- Dedication -- Contents -- Contributors -- Foreword -- Acknowledgments -- 1 - Personal and historical recollections of the early years of mass cytometry -- The evolution of DVS Sciences -- The culture of the early mass cytometry team -- Lessons learned/advice to an entrepreneur -- A short overview of the CyTOF technology -- A short overview of the MAXPAR technology -- References -- 2 - Unveiling spatial biology of cellular landscapes with imaging mass cytometry -- Introduction to imaging mass cytometry -- Overview -- Principles of imaging mass cytometry -- How imaging mass cytometry works -- History of imaging mass cytometry -- Features of imaging mass cytometry -- Imaging mass cytometry workflow -- Multiplex antibody panel design -- Staining tissues -- Image acquisition -- Image analysis -- IMC reveals the secrets of spatial biology in tissues -- Physiology of normal tissue -- Cancer -- Breast cancer -- Colorectal cancer -- Lung cancer -- Melanoma -- Brain cancer -- Preclinical tumor studies with model organisms -- Neurodegenerative diseases -- Parkinson's disease -- Multiple sclerosis -- Inflammatory diseases -- Future of imaging mass cytometry -- Summary -- Acknowledgments -- References -- 3 - Single-cell spatial phenotype mapping of tissue microenvironments with multiplexed ion beam imaging (MIBI): A highly multiplexed, high-resolution spatial proteomic approach for tissue imaging and analysis -- Introduction -- Importance of spatial context in tissue biology -- Limitations of traditional tissue analysis -- Emergence of multiplexed tissue imaging for spatial biology -- Fundamental principles of MIBI -- MIBI leverages mass spectrometry. , MIBI analysis involves a targeted immunoassay for protein marker identifiers of cell phenotype and state -- Aspects of MIBI analysis -- The MIBI workflow -- Components of the MIBI platform -- Considerations for experimental design -- MIBI data analysis -- Applications | Unlocking unchartered biology with MIBI -- Revealing the tumor-immune microenvironment structures of triple negative breast cancer -- Revealing spatial signatures of progression from DCIS to invasive breast cancer -- Revealing signatures linked to metastasis and immunosuppression in lung cancer -- Monitoring immune response in tumor therapy development -- Spatial metabolic profiling of cytotoxic T cells in human colorectal carcinoma -- Understanding the inflammatory state of immunotherapy-driven gastritis -- Exploring the immunoregulatory landscape of tuberculosis granulomas -- Investigating the orchestrated immune events of viral persistence in retroviral infection -- Capturing human neuropathology in neurodegenerative disease -- Conclusion -- Glossary -- References -- 4 - Highly multiplexed spatial protein data using CODEX technology -- Introduction -- Fundamental principles of CODEX -- Strengths and limitations of CODEX technology -- Codex instrument -- Considerations for experimental design -- CODEX data collection -- Data analysis-Tools and tips -- Visualizing unchartered biology -- Future directions -- Glossaries -- References -- Further reading -- 5 - Exploring uncharted spatial biology with ChipCytometry highly multiplexed imaging -- Introduction -- Fundamental principles of ChipCytometry -- ChipCytometry workflow -- Methods for signal removal -- Technique strengths and limitations -- Increasing plex through cycle count -- Antibodies from any commercial vendor -- Walk-away automation -- High-throughput imaging -- Subcellular imaging -- Multiexposure HDR image fusion. , Equipment involved -- Biological materials and applications -- Fluorescent antibodies -- Imaging with CellScape -- Microfluidics unit -- CellScape microfluidic chip -- Experimental design considerations -- Antibody validation for ChipCytometry -- ChipCytometry antibody panel design -- Optimizing antigen retrieval -- Experimental data collection -- Image acquisition -- Image processing -- Cell segmentation -- Cell phenotyping -- Visualizing unchartered biology -- References -- 6 - Combined nucleic acid and protein quantification in the native tissue microenvironment -- Introduction -- Immuno-fluorescence-based multiplexed IHC -- Multiplexed IHC by rasterization and mass spectrometry -- Highly multiplexed fluorescence in situ hybridization -- Other strategies -- Combined spatial-omics -- Computational tools -- Conclusions -- Acknowledgments -- References -- 7 - Tissue schematics: Representing tissues as assemblies of neighborhoods -- Introduction -- Principles underlying tissue schematics -- Strengths and limitations -- Experimental context considerations -- Technical considerations -- Equipment involved -- Experiment design considerations -- Constructing tissue schematics -- Identifying cell types -- Identifying cellular neighborhoods -- Identifying spatial contexts -- Indexing tissue motifs -- Identifying assembly rules -- Interpreting tissue schematics -- Interpreting cellular neighborhoods -- Interpreting spatial contexts -- Interpreting assembly rules -- Uncharted biology visualized by tissue schematics -- Key terms and definitions -- References -- 8 - High-definition CODEX for 3D multiplex spatial cell phenotyping -- Introduction -- CODEX principles, strengths, and limitations -- Experimental design, equipment, and considerations -- Visualizing uncharted biology. , HD-CODEX allows for multiplexing protein targets in tissues at unprecedented resolution -- HD-CODEX provides insight into significant cell-cell spatial differences in 3D protein expression -- Advice for novice CODEX and HD-CODEX users -- Future directions -- Key terms and definitions -- Omics -- Proteomics -- Sequencing -- Phenotyping -- Clustering -- Image resolution -- Cell segmentation -- Fluorescence microscopy -- Antibody -- Reagent -- Hypothesis test -- Null hypothesis -- Uniform manifold approximation and projection -- Wilcoxon signed-rank test -- Jaccard index -- Kolmogorov-Smirnov hypothesis test -- Z-stack -- References -- Index -- Back Cover.

Additional Edition: Print version: Fantl, Wendy Revealing Uncharted Biology with Single Cell Multiplex Proteomic Technologies San Diego : Elsevier Science & Technology,c2024 ISBN 9780128222096

Language: English