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knowledge-base-manifest.yaml
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name: "BioImage.IO Knowledge Base"
description: "A knowledge base for models, tools, workflows etc. for computational bioimaging"
format_version: "0.1.0"
collections:
- name: ilastik
id: ilastik
source: https://github.com/ilastik/ilastik.github.io/archive/30b5ccbde9b7ce100259480019662be89a5a1f32.zip
directory: documentation
description: ilastik - the interactive learning and segmentation toolkit, Leverage machine learning algorithms to easily segment, classify, track and count your cells or other experimental data
base_url: https://www.ilastik.org/documentation/
authors:
- name: ilastik Team
license: "[GPLv2](https://www.ilastik.org/license)"
reference: "https://www.ilastik.org/documentation/"
format: markdown
- name: BioImage.IO
id: bioimage.io
source: https://github.com/bioimage-io/bioimage.io/archive/8ce3559d80f500eb34e1f75d9ea776d6efed5aef.zip
directory: docs
description: A platform for sharing and deploying deep learning models in bioimaging.
base_url: https://bioimage.io/docs/
authors:
- name: BioImage.IO Team
license: "[MIT License](https://github.com/bioimage-io/bioimage.io?tab=MIT-1-ov-file#readme)"
reference: "https://bioimage.io/docs/"
format: markdown
- name: imagej.net
id: imagej.net
source: https://github.com/imagej/imagej.github.io/archive/7bdb57db2f0c616a21742611f534bbe2fd215416.zip
directory: _pages
description: The ImageJ wiki with a lot of useful information about ImageJ, Fiji and related plugins and tools.
base_url: https://imagej.net
authors:
- name: ImageJ Team
license: "[Creative Commons Attribution 3.0 Unported](https://github.com/imagej/imagej.github.io?tab=License-1-ov-file#readme)"
reference: "https://github.com/imagej/imagej.github.io?tab=readme-ov-file"
format: markdown
- name: bio.tools
id: bio.tools
source: https://github.com/research-software-ecosystem/content/archive/954c3b2da10e951b2fbcf17825013c1c44ceddf6.zip
directory: data
description: A repository for research software tools with metadata.
base_url: https://bio.tools
authors:
- name: bio.tools Team
license: "[CC BY 4.0](https://biotools.readthedocs.io/en/latest/license.html)"
reference: "https://biotools.readthedocs.io/en/latest/index.html"
format: json
- name: ImJoy
id: imjoy
source: https://github.com/imjoy-team/ImJoy/archive/c255d9cda9dc19d441fb7cf1eaca806e5ec71af8.zip
directory: docs
description: A plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools.
base_url: https://imjoy.io/docs/#/
authors:
- name: ImJoy Team
license: "[MIT License](https://imjoy.io/docs/#/?id=license)"
reference: "https://imjoy.io/docs/#/"
format: markdown
- name: deepImageJ
id: deepimagej
source: https://s3.imjoy.io/public-datasets/deepimagej-plugin.wiki.zip
directory: "."
description: The ImageJ plugin to run deep-learning models
base_url: https://deepimagej.github.io/
authors:
- name: DeepImageJ Team
license: "[BSD 2-Clause](https://github.com/deepimagej/deepimagej-plugin/blob/master/LICENSE)"
reference: "https://deepimagej.github.io/about.html"
format: markdown
- name: scikit-image
id: scikit-image
source: https://raw.githubusercontent.com/oeway/hypha-knowledge-base/gh-pages/scikit-image-0.21.0.pdf
description: A collection of algorithms for image processing.
base_url: https://scikit-image.org/docs/stable/
authors:
- name: Stefan van der Walt
organization: University of California, Berkeley
- name: Juan Nunez-Iglesias
organization: Monash University
- name: et al.
license: "[BSD 3-Clause](https://github.com/scikit-image/scikit-image?tab=License-1-ov-file#readme)"
reference: "https://github.com/scikit-image/scikit-image?tab=readme-ov-file"
format: pdf
- name: napari
id: napari
source: https://github.com/napari/docs/archive/be52ea709193a45ced6359f7f3feb197cc8dbb3a.zip
directory: docs
description: napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images.
base_url: https://napari.org/stable/
authors:
- name: napari Team
license: "[BSD 3-Clause](https://github.com/napari/napari?tab=BSD-3-Clause-1-ov-file#readme)"
reference: "https://github.com/napari/napari?tab=readme-ov-file"
format: markdown
- name: Introduction to Bioimage Analysis
id: book-itba
source: https://github.com/bioimagebook/bioimagebook.github.io/archive/9519fb297cece3a131718a36f642ba463c41b160.zip
directory: chapters
description: "A book written by Pete Bankhead about introduction to bioimage analysis, including practical exercises and Jupyter Book content"
base_url: https://bioimagebook.github.io/
authors:
- name: Pete Bankhead
organization: University of Edinburgh
license: "[CC BY 4.0](https://bioimagebook.github.io/chapters/0-preamble/license.html)"
reference: "https://bioimagebook.github.io/"
format: markdown
- name: Deep Learning for Medical Image Analysis
id: book-dlfmia
source: https://raw.githubusercontent.com/oeway/hypha-knowledge-base/gh-pages/deep-learning-for-medical-image-analysis-1nbsped-0128104082-978-0-12-810408-8_compress.pdf
description: "A book written by S. Kevin Zhou, Hayit Greenspan, Dinggang Shen about deep learning for medical image analysis"
base_url: https://www.elsevier.com/books/deep-learning-for-medical-image-analysis/zhou/978-0-12-810408-8
authors:
- name: S. Kevin Zhou
organization: University of Science and Technology of China
- name: Hayit Greenspan
organization: Tel Aviv University
- name: Dinggang Shen
organization: ShanghaiTech University
license: "[All rights reserved]"
reference: "https://www.elsevier.com/books/deep-learning-for-medical-image-analysis/zhou/978-0-12-810408-8"
format: pdf
- name: How deep learning is used within microscopy
id: book-hdluwm
source: https://raw.githubusercontent.com/oeway/hypha-knowledge-base/gh-pages/Nikon-Deep-Learning-ebook-compressed.pdf
description: "A book written by Nikon about how deep learning is used within microscopy"
base_url: https://www.microscope.healthcare.nikon.com/resources/ebooks/how-deep-learning-is-used-within-microscopy
authors:
- name: Nikon
organization: Nikon
license: "[All rights reserved]"
reference: "https://www.microscope.healthcare.nikon.com/resources/ebooks/how-deep-learning-is-used-within-microscopy"
format: pdf
- name: BioImage Data Analysis
id: book-bda
source: https://raw.githubusercontent.com/oeway/hypha-knowledge-base/gh-pages/bioimagedataanalysis-compressed.pdf
description: "A book about bioimage data analysis"
base_url: https://analyticalscience.wiley.com/content/article-do/bioimage-data-analysis
authors:
- name: Kota Miura (editor) et al.
organization: Nikon Imaging Center, Heidelberg
reference: "https://analyticalscience.wiley.com/content/article-do/bioimage-data-analysis"
license: "[All rights reserved]"
format: pdf
- name: Deep Learning in Medical Imaging
id: book-dlmi
source: https://raw.githubusercontent.com/oeway/hypha-knowledge-base/gh-pages/Deep%20Learning%20in%20Medical%20Imaging.pdf
description: "A book written by Narjes Benameur and Ramzi Mahmoudi about deep learning in medical imaging"
base_url: https://www.intechopen.com/chapters/87248
authors:
- name: Narjes Benameur
organization: University of Tunis el Manar
- name: Ramzi Mahmoudi
organization: University of Monastir, Tunisia
license: "[Licensee IntechOpen. Creative Commons Attribution 3.0 License](https://www.intechopen.com/chapters/87248)"
reference: "https://www.intechopen.com/chapters/87248"
format: pdf
- name: FUTURE AI International consensus guideline for trustworthy and deployable AI in healthcare
id: book-fat
source: https://raw.githubusercontent.com/oeway/hypha-knowledge-base/gh-pages/FUTURE%20AI%20International%20consensus%20guideline%20for%20trustworthy%20and%20deployable%20artificial%20intelligence%20in%20healthcare.pdf
description: "An article written by the FUTURE AI consortium about international consensus guideline for trustworthy and deployable artificial intelligence in healthcare"
base_url: https://arxiv.org/abs/2309.12325
authors:
- name: Karim Lekadir
organization: University of Barcelona
- name: Aasa Feragen
organization: Technical University of Denmark
- name: et al.
license: "[arXiv.org perpetual, non-exclusive license 1.0](https://arxiv.org/licenses/nonexclusive-distrib/1.0/license.html)"
reference: "https://arxiv.org/abs/2309.12325"
format: pdf
- name: Roadmap on Deep Learning for Microscopy
id: book-rdlfm
source: https://raw.githubusercontent.com/oeway/hypha-knowledge-base/gh-pages/Roadmap%20on%20Deep%20Learning%20for%20Microscopy-compressed.pdf
description: "An article written by Giovanni Volpe, et al. about roadmap on deep learning for microscopy"
base_url: https://arxiv.org/abs/2303.03793
authors:
- name: Giovanni Volpe
organization: University of Gothenburg
- name: Carolina Wählby
organization: Uppsala University
- name: Lei Tian
organization: Boston University
- name: et al.
license: "[arXiv.org perpetual, non-exclusive license 1.0](https://arxiv.org/licenses/nonexclusive-distrib/1.0/license.html)"
reference: "https://arxiv.org/abs/2303.03793"
format: pdf
- name: The Rise of Data-Driven Microscopy powered by Machine Learning
id: book-tddmpml
source: https://raw.githubusercontent.com/oeway/hypha-knowledge-base/gh-pages/The%20Rise%20of%20Data-Driven%20Microscopy%20powered%20by%20Machine%20Learning.pdf
description: "An article written by Leonor Morgado, et al. about the rise of data-driven microscopy powered by machine learning"
base_url: https://onlinelibrary.wiley.com/doi/full/10.1111/jmi.13282
authors:
- name: Leonor Morgado
organization: Instituto Gulbenkian de Ciência, Oeiras, Portugal
- name: Estibaliz Gómez-de-Mariscal
organization: Instituto Gulbenkian de Ciência, Oeiras, Portugal
- name: Hannah S. Heil
organization: Instituto Gulbenkian de Ciência, Oeiras, Portugal
- name: Ricardo Henriques
organization: Instituto Gulbenkian de Ciência, Oeiras, Portugal
license: "[All rights reserved]"
reference: "https://onlinelibrary.wiley.com/doi/full/10.1111/jmi.13282"
format: pdf
- name: The ITK Software Guide Book 1 Introduction and Development Guidelines
id: book-isg1idg
source: https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/releases/download/v5.3.0/InsightSoftwareGuide-Book1-5.3.0.pdf
description: "Introduction to ITK, how to install, build, basis system concepts, design of data structures and application of analysis methods, and how to contribute"
base_url: https://docs.itk.org
authors:
- name: Hans J. Johnson
organization: University of Iowa
- name: Matthew M. McCormick
organization: Kitware
- name: Luis Ibáñez
organization: Google LLC
- name: Insight Software Consortium
license: "[Apache 2.0](https://github.com/InsightSoftwareConsortium/ITK?tab=Apache-2.0-1-ov-file)"
reference: "https://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1.html"
format: pdf
- name: The ITK Software Guide Book 2 Design and Functionality
id: book-isg2df
source: https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/releases/download/v5.3.0/InsightSoftwareGuide-Book2-5.3.0.pdf
description: "Detailed design and functionality for reading and writing images, filtering, registration, segmentation, and performing statistical analysis"
base_url: https://docs.itk.org
authors:
- name: Hans J. Johnson
organization: University of Iowa
- name: Matthew M. McCormick
organization: Kitware
- name: Luis Ibáñez
organization: Google LLC
- name: Insight Software Consortium
license: "[Apache 2.0](https://github.com/InsightSoftwareConsortium/ITK?tab=Apache-2.0-1-ov-file)"
reference: "https://itk.org/ITKSoftwareGuide/html/Book2/ITKSoftwareGuide-Book2.html"
format: pdf
- name: ITK
id: itk
source: https://github.com/InsightSoftwareConsortium/ITK/archive/4d750726d06ba28c601b8a4bfac8780baa395ff1.zip
directory: Documentation/docs
description: "ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions"
base_url: https://docs.itk.org
authors:
- name: Insight Software Consortium
license: "[Apache 2.0](https://github.com/InsightSoftwareConsortium/ITK?tab=Apache-2.0-1-ov-file)"
reference: "https://github.com/InsightSoftwareConsortium/ITK"
format: markdown
- name: ITK-Wasm
id: itkwasm
source: https://github.com/InsightSoftwareConsortium/itk-wasm/archive/169a2e0eed6b30d91c59081643668ef13045bb93.zip
directory: docs
description: "High-performance spatial analysis in a web browser, Node.js, and across programming languages and hardware architectures"
base_url: https://wasm.itk.org
authors:
- name: Insight Software Consortium
license: "[Apache 2.0](https://github.com/InsightSoftwareConsortium/itk-wasm?tab=Apache-2.0-1-ov-file#readme)"
reference: "https://github.com/InsightSoftwareConsortium/itk-wasm"
format: markdown
additional_channels:
- name: "biii.eu"
id: biii.eu
description: "The BioImage Informatics Index"