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oapen-20.500.12657-586152022-10-15T03:13:36Z Bioimage Data Analysis Workflows ‒ Advanced Components and Methods Miura, Kota Sladoje, Nataša Analyzing Image Data in Biology Building a Bioimage Analysis Workflow Computational Analysis Chosing the Correct Components for Given Biological Questions Data Handling and Plotting Deep Learning Fast Computation GPU-Acceleration Handling Biological data Machine Learning Phyton Processing Language Understanding Bioimage Analysis Software bic Book Industry Communication::P Mathematics & science::PS Biology, life sciences::PSF Cellular biology (cytology) bic Book Industry Communication::P Mathematics & science::PS Biology, life sciences::PSD Molecular biology bic Book Industry Communication::P Mathematics & science::PN Chemistry::PNF Analytical chemistry bic Book Industry Communication::P Mathematics & science::PS Biology, life sciences This open access textbook aims at providing detailed explanations on how to design and construct image analysis workflows to successfully conduct bioimage analysis. Addressing the main challenges in image data analysis, where acquisition by powerful imaging devices results in very large amounts of collected image data, the book discusses techniques relying on batch and GPU programming, as well as on powerful deep learning-based algorithms. In addition, downstream data processing techniques are introduced, such as Python libraries for data organization, plotting, and visualizations. Finally, by studying the way individual unique ideas are implemented in the workflows, readers are carefully guided through how the parameters driving biological systems are revealed by analyzing image data. These studies include segmentation of plant tissue epidermis, analysis of the spatial pattern of the eye development in fruit flies, and the analysis of collective cell migration dynamics. The presented content extends the Bioimage Data Analysis Workflows textbook (Miura, Sladoje, 2020), published in this same series, with new contributions and advanced material, while preserving the well-appreciated pedagogical approach adopted and promoted during the training schools for bioimage analysis organized within NEUBIAS – the Network of European Bioimage Analysts. This textbook is intended for advanced students in various fields of the life sciences and biomedicine, as well as staff scientists and faculty members who conduct regular quantitative analyses of microscopy images. 2022-10-14T10:39:12Z 2022-10-14T10:39:12Z 2022 book ONIX_20221014_9783030763947_6 9783030763947 https://library.oapen.org/handle/20.500.12657/58615 eng Learning Materials in Biosciences application/pdf n/a 978-3-030-76394-7.pdf https://link.springer.com/978-3-030-76394-7 Springer Nature Springer 10.1007/978-3-030-76394-7 10.1007/978-3-030-76394-7 6c6992af-b843-4f46-859c-f6e9998e40d5 6acec104-222c-4e0b-ac1f-a1d9050064a0 9783030763947 Springer 212 Cham [...] open access
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This open access textbook aims at providing detailed explanations on how to design and construct image analysis workflows to successfully conduct bioimage analysis. Addressing the main challenges in image data analysis, where acquisition by powerful imaging devices results in very large amounts of collected image data, the book discusses techniques relying on batch and GPU programming, as well as on powerful deep learning-based algorithms. In addition, downstream data processing techniques are introduced, such as Python libraries for data organization, plotting, and visualizations. Finally, by studying the way individual unique ideas are implemented in the workflows, readers are carefully guided through how the parameters driving biological systems are revealed by analyzing image data. These studies include segmentation of plant tissue epidermis, analysis of the spatial pattern of the eye development in fruit flies, and the analysis of collective cell migration dynamics. The presented content extends the Bioimage Data Analysis Workflows textbook (Miura, Sladoje, 2020), published in this same series, with new contributions and advanced material, while preserving the well-appreciated pedagogical approach adopted and promoted during the training schools for bioimage analysis organized within NEUBIAS – the Network of European Bioimage Analysts. This textbook is intended for advanced students in various fields of the life sciences and biomedicine, as well as staff scientists and faculty members who conduct regular quantitative analyses of microscopy images.
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