From 672180f22d66866636e5acf97cfb0392ce8d6930 Mon Sep 17 00:00:00 2001 From: alalulu8668 Date: Sat, 10 Aug 2024 20:45:54 +0200 Subject: [PATCH 01/10] add acknowledgement for articles/books --- knowledge-base-manifest.yaml | 105 ++++++++++++++++++++++++++++++++--- 1 file changed, 96 insertions(+), 9 deletions(-) diff --git a/knowledge-base-manifest.yaml b/knowledge-base-manifest.yaml index 31012aa..71953a7 100644 --- a/knowledge-base-manifest.yaml +++ b/knowledge-base-manifest.yaml @@ -63,60 +63,140 @@ collections: 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" + 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/en_EU/products/software/deep-learning + 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 written by Kota Miura about bioimage data analysis" base_url: https://analyticalscience.wiley.com/content/article-do/bioimage-data-analysis + authors: + - name: Kota Miura + 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 Daniel K. Sodickson, MD, PhD, and W. Clem Karl, PhD about deep learning in medical imaging" + description: "A book written by Narjes Benameur and Ramzi Mahmoudi about deep learning in medical imaging" base_url: https://www.rsna.org/-/media/Files/RSNA/Education/RSNA-Press/Deep-Learning-in-Medical-Imaging.pdf + 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" + 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: "A book written by the FUTURE AI consortium about international consensus guideline for trustworthy and deployable artificial intelligence in healthcare" - base_url: https://www.nature.com/articles/s41591-021-01412-4 + 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" + 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: "A book written by the FUTURE AI consortium about international consensus guideline for trustworthy and deployable artificial intelligence in healthcare" - base_url: https://www.nature.com/articles/s41592-021-01108-9 + 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" + 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: "A book written by the FUTURE AI consortium about international consensus guideline for trustworthy and deployable artificial intelligence in healthcare" - base_url: https://www.nature.com/articles/s41592-021-01108-9 + 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" + 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" + reference: "https://itk.org/ITKSoftwareGuide/html/Book2/ITKSoftwareGuide-Book2.html" format: pdf - name: ITK id: itk @@ -124,6 +204,10 @@ collections: 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" + reference: "https://github.com/InsightSoftwareConsortium/ITK" format: markdown - name: ITK-Wasm id: itkwasm @@ -131,8 +215,11 @@ collections: 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" + reference: "https://github.com/InsightSoftwareConsortium/itk-wasm" format: markdown - additional_channels: - name: "biii.eu" id: biii.eu From caf8bbbc7f811a597c39309e44011f68503cb8b4 Mon Sep 17 00:00:00 2001 From: Wei Ouyang Date: Sat, 10 Aug 2024 13:23:26 -0700 Subject: [PATCH 02/10] Add acknowledgements --- bioimageio_chatbot/chatbot.py | 2 +- .../chatbot_extensions/docs_extension.py | 12 +++ bioimageio_chatbot/static/index.html | 74 +++++++++++++++++++ bioimageio_chatbot/utils.py | 1 + 4 files changed, 88 insertions(+), 1 deletion(-) diff --git a/bioimageio_chatbot/chatbot.py b/bioimageio_chatbot/chatbot.py index bda9c1d..3995d2f 100644 --- a/bioimageio_chatbot/chatbot.py +++ b/bioimageio_chatbot/chatbot.py @@ -215,7 +215,7 @@ class ThoughtsSchema(BaseModel): # convert to a list all_extensions = [ - {"id": ext.id, "name": ext.name, "description": ext.description} for ext in builtin_extensions + {"id": ext.id, "name": ext.name, "description": ext.description, "info": ext.info} for ext in builtin_extensions ] # remove item with 'book' in all_extensions melman_extensions = [ diff --git a/bioimageio_chatbot/chatbot_extensions/docs_extension.py b/bioimageio_chatbot/chatbot_extensions/docs_extension.py index b9d740b..0c2f1f1 100644 --- a/bioimageio_chatbot/chatbot_extensions/docs_extension.py +++ b/bioimageio_chatbot/chatbot_extensions/docs_extension.py @@ -121,6 +121,8 @@ async def run_extension( run_extension.__doc__ = f"""Searching documentation for {channel_id}: {collection['description']}.{base_url_prompt}""" return schema_tool(run_extension) +INFO_KEYS = ["name","description", "authors", "license", "reference"] + def get_extension(): collections = get_manifest()["collections"] knowledge_base_path = os.environ.get( @@ -141,12 +143,20 @@ def get_extension(): docs_store_dict = load_knowledge_base(knowledge_base_path) docs_tools = {} + docs_info = {} books_tools = {} + books_info = {} for col in collections: + info = {k: col[k] for k in INFO_KEYS if k in col} if "book" in col["id"]: books_tools["search_" + col["id"]] = create_tool(docs_store_dict, col) + if info: + books_info["search_" + col["id"]] = info else: docs_tools["search_" + col["id"]] = create_tool(docs_store_dict, col) + if info: + docs_info["search_" + col["id"]] = info + if docs_tools: sinfo1 = ChatbotExtension( @@ -154,6 +164,7 @@ def get_extension(): name="Search BioImage Docs", description="Search information in the documents of the bioimage.io knowledge base. Provide a list of keywords to search information in the documents. Returns a list of relevant documents.", tools=docs_tools, + info=docs_info ) if books_tools: sinfo2 = ChatbotExtension( @@ -161,6 +172,7 @@ def get_extension(): name="Search BioImage Books", description="Search information in BioImage books. Provide a list of keywords to search information in the books. Returns a list of relevant documents.", tools=books_tools, + info=books_info ) return sinfo1, sinfo2 diff --git a/bioimageio_chatbot/static/index.html b/bioimageio_chatbot/static/index.html index da34a88..7111903 100644 --- a/bioimageio_chatbot/static/index.html +++ b/bioimageio_chatbot/static/index.html @@ -491,6 +491,7 @@

Welcome to BioImage.IO Chatbot


Extensions: +
@@ -1607,6 +1608,7 @@

Welcome to BioImage.IO Chatbot

} } updateDropdownOptions(extensions); + updateAboutExtensions(extensions); showReadyStatus(); appendRobotMessage(allAssistants[assistantName]['welcome_message'], "message-0"); // Append robot message to the message container return svc; @@ -1686,6 +1688,78 @@

Welcome to BioImage.IO Chatbot

return '' + text + ''; } + function updateAboutExtensions(extensions) { + $('#about-extensions').empty(); + + // Create the card structure + const card = document.createElement('div'); + card.className = 'card'; + const cardHeader = ` +
+ BioImage.IO Icon + About BioImage.IO Chatbot Extensions +
`; + + const cardBody = document.createElement('div'); + cardBody.className = 'card-body'; + + // Add leading text + const leadingText = ` +
+

Our chatbot is enhanced by a diverse set of extensions that utilize the following valuable sources. We extend our sincere gratitude to all contributors, particularly the original authors whose works have significantly enriched this project. These sources are primarily used for research purposes, in accordance with the European Union's copyright exception on Text and Data Mining (TDM) under Directive (EU) 2019/790.

+

If you are an author of any material used within these extensions and wish to have your content removed or updated, we respectfully request that you contact us directly. We will promptly address your concerns and ensure that your material is removed from our system.

+

Notice: Users of this chatbot are kindly reminded to carefully check with the original sources for accuracy and completeness. For any work derived from these sources, please ensure that you respect their respective licenses and adhere to the conditions set forth by the original authors.

+
`; + + // Append title and leading text to the card body + cardBody.innerHTML = leadingText; + + // Initialize a markdown renderer + const renderer = new marked.Renderer(); + + for (const ext of extensions) { + const extInfo = document.createElement('div'); + + // Start creating markdown content with improved formatting + let markdownContent = `### ${ext.name} 📚\n\n#### ${ext.description}\n\n`; + + // Iterate through each tool in the extension info + for (const [key, tool] of Object.entries(ext.info)) { + markdownContent += `----\n**${tool.name} 🛠️**\n\n`; + markdownContent += `**📝 Description**: ${tool.description}\n\n`; + + markdownContent += `**👥 Authors**:\n`; + for (const author of tool.authors) { + markdownContent += `- ${author.name}, *${author.organization}*\n`; + } + + markdownContent += `\n**📜 License**: ${tool.license}\n\n`; + markdownContent += `**🔗 [Reference](${tool.reference})**: ${tool.reference}\n\n`; + } + + // Convert markdown content to HTML using marked + const renderedContent = marked(markdownContent, { renderer: renderer }); + + // Wrap the content in a collapsible
block + extInfo.innerHTML = ` +
+ Extension: ${ext.name} + ${renderedContent} +
+ `; + + // Append the rendered content to the card body + cardBody.appendChild(extInfo); + } + + // Combine the card structure + card.innerHTML = cardHeader; + card.appendChild(cardBody); + + // Append the entire card to the about-extensions section + $('#about-extensions').append(card); + } + function autoResize() { this.style.height = (this.scrollHeight) + 'px'; } diff --git a/bioimageio_chatbot/utils.py b/bioimageio_chatbot/utils.py index be5fcb1..27a005a 100644 --- a/bioimageio_chatbot/utils.py +++ b/bioimageio_chatbot/utils.py @@ -65,6 +65,7 @@ class ChatbotExtension(BaseModel): tools: Optional[Dict[str, Any]] = {} get_schema: Optional[Callable] = None get_state: Optional[Callable] = None + info: Optional[Dict[str, Any]] = {} class LegacyChatbotExtension(BaseModel): """A class that defines the interface for a user extension""" From 119e80fe984c9505c2021a36c96fce4981cd18a7 Mon Sep 17 00:00:00 2001 From: Wei Ouyang Date: Sat, 10 Aug 2024 13:43:07 -0700 Subject: [PATCH 03/10] Remove KB links for download --- bioimageio_chatbot/knowledge_base.py | 10 ++-------- docs/README.md | 15 +++++++++++++++ 2 files changed, 17 insertions(+), 8 deletions(-) diff --git a/bioimageio_chatbot/knowledge_base.py b/bioimageio_chatbot/knowledge_base.py index f290de0..73400c8 100644 --- a/bioimageio_chatbot/knowledge_base.py +++ b/bioimageio_chatbot/knowledge_base.py @@ -11,20 +11,14 @@ import pickle from bioimageio_chatbot.utils import get_manifest, download_file -KNOWLEDGE_BASE_URL = os.environ.get("BIOIMAGEIO_KNOWLEDGE_BASE_URL", "https://uk1s3.embassy.ebi.ac.uk/public-datasets/bioimageio-knowledge-base") - def load_docs_store(db_path, collection_name): # Each collection has two files [collection_name].faiss and [collection_name].pkl # Check if it exists, otherwise, download from {KNOWLEDGE_BASE_URL}/[collection].faiss if not os.path.exists(os.path.join(db_path, f"{collection_name}.faiss")): - print(f"Downloading {collection_name}.faiss from {KNOWLEDGE_BASE_URL}/{collection_name}.faiss") - download_file(f"{KNOWLEDGE_BASE_URL}/{collection_name}.faiss", os.path.join(db_path, f"{collection_name}.faiss")) - + raise Exception(f"Please build the docs store {collection_name} by running create_vector_knowledge_base first.") if not os.path.exists(os.path.join(db_path, f"{collection_name}.pkl")): - print(f"Downloading {collection_name}.pkl from {KNOWLEDGE_BASE_URL}/{collection_name}.pkl") - download_file(f"{KNOWLEDGE_BASE_URL}/{collection_name}.pkl", os.path.join(db_path, f"{collection_name}.pkl")) - + raise Exception(f"Please build the docs store {collection_name} by running create_vector_knowledge_base first.") # Load from vector store embeddings = OpenAIEmbeddings() docs_store = FAISS.load_local(index_name=collection_name, folder_path=db_path, embeddings=embeddings, allow_dangerous_deserialization=True) diff --git a/docs/README.md b/docs/README.md index c0a9c00..2a07ec6 100644 --- a/docs/README.md +++ b/docs/README.md @@ -121,3 +121,18 @@ We thank [AI4Life consortium](https://ai4life.eurobioimaging.eu/) for its crucia ![AI4Life](https://ai4life.eurobioimaging.eu/wp-content/uploads/2022/09/AI4Life-logo_giraffe-nodes-2048x946.png) AI4Life has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement number 101057970. Views and opinions expressed are, however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. + +## Disclaimer + +The BioImage.IO Chatbot is greatly enriched by the valuable resources contributed by the global bioimage analysis community. We extend our deepest gratitude to all contributors, especially the original authors of the materials integrated into our extensions. Their work has significantly enhanced the capabilities of this chatbot, providing users with high-quality information and tools. + +These resources are primarily utilized for research purposes in compliance with the European Union's copyright exception on Text and Data Mining (TDM) as outlined in [Directive (EU) 2019/790](https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX%3A32019L0790). + +The full list of sources and resources used by the BioImage.IO Chatbot can be found in our [knowledge base manifest](https://github.com/bioimage-io/bioimageio-chatbot/blob/main/knowledge-base-manifest.yaml). We kindly ask users to carefully verify the accuracy and completeness of information with the original sources. For any work derived from these resources, please ensure that you respect the respective licenses and adhere to the conditions set forth by the original authors. + +If you are an author of any material used within the BioImage.IO Chatbot and wish to have your content removed, please contact us directly. We are committed to respecting the rights of all contributors and will promptly address your request. + +We would also like to thank the open-source community for their ongoing support and innovation, which continuously drives the development and improvement of the BioImage.IO platform. + +Thank you for supporting the BioImage.IO project and contributing to the advancement of bioimage analysis! + From b476150343b6aa7277d4ef6f26dacfde9065f185 Mon Sep 17 00:00:00 2001 From: Wei Ouyang Date: Sat, 10 Aug 2024 14:03:35 -0700 Subject: [PATCH 04/10] Update disclaimer --- bioimageio_chatbot/static/index.html | 36 +++++++++++++--------------- docs/DISCLAIMER.md | 13 ++++++++-- docs/README.md | 15 ++++-------- 3 files changed, 32 insertions(+), 32 deletions(-) diff --git a/bioimageio_chatbot/static/index.html b/bioimageio_chatbot/static/index.html index 7111903..3b55f59 100644 --- a/bioimageio_chatbot/static/index.html +++ b/bioimageio_chatbot/static/index.html @@ -341,12 +341,7 @@ for each response, or by clicking the 'Feedback' button below.

- -

Note that the chatbot is still in beta and is being actively developed, we will log the message you input into - the chatbot for further investigation of issues and support our development. See the - Disclaimer for more details. If you want to to remove your chat logs, please contact us via this form.

+

Note that the BioImage.IO Chatbot is part of a research project focused on Text and Data Mining (TDM) and is still in beta, being actively developed. The chatbot is intended for research and educational purposes only and is not meant for production or commercial use. We log the messages you input into the chatbot to support ongoing research, improve the service, and investigate any issues. Please be aware that the chatbot utilizes copyrighted materials under the EU's TDM exception. For more details, see the Disclaimer. If you are an author and wish to opt-out your material or if you want your chat logs removed, please contact us via this form.

@@ -1704,12 +1699,11 @@

Welcome to BioImage.IO Chatbot

cardBody.className = 'card-body'; // Add leading text - const leadingText = ` -
-

Our chatbot is enhanced by a diverse set of extensions that utilize the following valuable sources. We extend our sincere gratitude to all contributors, particularly the original authors whose works have significantly enriched this project. These sources are primarily used for research purposes, in accordance with the European Union's copyright exception on Text and Data Mining (TDM) under Directive (EU) 2019/790.

-

If you are an author of any material used within these extensions and wish to have your content removed or updated, we respectfully request that you contact us directly. We will promptly address your concerns and ensure that your material is removed from our system.

-

Notice: Users of this chatbot are kindly reminded to carefully check with the original sources for accuracy and completeness. For any work derived from these sources, please ensure that you respect their respective licenses and adhere to the conditions set forth by the original authors.

-
`; + const leadingText = `
+

Our chatbot is enhanced by a diverse set of extensions that utilize the following valuable sources. We extend our sincere gratitude to all contributors, particularly the original authors whose works have significantly enriched this project. These sources are primarily used for research purposes, in accordance with the European Union's copyright exception on Text and Data Mining (TDM) under Directive (EU) 2019/790.

+

If you are an author of any material used within these extensions and wish to have your content removed or updated, we respectfully request that you contact us directly. You can do so via this form. We will promptly address your concerns and ensure that your material is removed from our system.

+

Notice: Users of this chatbot are kindly reminded to carefully check with the original sources for accuracy and completeness. For any work derived from these sources, please ensure that you respect their respective licenses and adhere to the conditions set forth by the original authors.

+
`; // Append title and leading text to the card body cardBody.innerHTML = leadingText; @@ -1727,14 +1721,18 @@

Welcome to BioImage.IO Chatbot

for (const [key, tool] of Object.entries(ext.info)) { markdownContent += `----\n**${tool.name} 🛠️**\n\n`; markdownContent += `**📝 Description**: ${tool.description}\n\n`; - - markdownContent += `**👥 Authors**:\n`; - for (const author of tool.authors) { - markdownContent += `- ${author.name}, *${author.organization}*\n`; + if(tool.authors && tool.authors.length > 0){ + markdownContent += `**👥 Authors**:\n`; + for (const author of tool.authors) { + markdownContent += `- ${author.name}, *${author.organization}*\n`; + } + } + if(tool.license){ + markdownContent += `**📜 License**: ${tool.license}\n\n`; + } + if (tool.reference) { + markdownContent += `**🔗 [Reference](${tool.reference})**: ${tool.reference}\n\n`; } - - markdownContent += `\n**📜 License**: ${tool.license}\n\n`; - markdownContent += `**🔗 [Reference](${tool.reference})**: ${tool.reference}\n\n`; } // Convert markdown content to HTML using marked diff --git a/docs/DISCLAIMER.md b/docs/DISCLAIMER.md index 8a6ef29..f9e3fa9 100644 --- a/docs/DISCLAIMER.md +++ b/docs/DISCLAIMER.md @@ -1,8 +1,16 @@ # Disclaimer for BioImage.IO Chatbot +## Research Purpose and Use of Copyrighted Material + +The BioImage.IO Chatbot ("Chatbot") is part of a research project focused on Text and Data Mining (TDM) to support advancements in bioimage analysis. The primary purpose of this Chatbot is to assist users in navigating resources, tools, and workflows related to bioimage analysis for research and educational purposes. In compliance with the European Union's copyright exception on TDM as outlined in [Directive (EU) 2019/790](https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX%3A32019L0790), the Chatbot utilizes copyrighted materials to which we have lawful access. These materials are used exclusively for non-commercial research purposes. + +## Evaluation-Only Use of Source Code and Live Demo + +The BioImage.IO Chatbot's source code and live demo instance are provided solely for evaluation purposes. These services are intended to support ongoing research in Text and Data Mining and are not intended for production use or commercial purposes. Users are encouraged to explore the capabilities of the Chatbot but should refrain from deploying it in any production environment or for commercial gain. + ## General Usage -The BioImage.IO Chatbot ("Chatbot") is intended for informational purposes only and aims to assist users in navigating the resources, tools, and workflows related to bioimage analysis. While we strive for accuracy, the Chatbot is not a substitute for professional advice, consultation, diagnosis, or any kind of formal scientific interpretation. +While we strive for accuracy, the Chatbot is not a substitute for professional advice, consultation, diagnosis, or any kind of formal scientific interpretation. Users should independently verify the accuracy and completeness of the information provided by the Chatbot. ## No Warranties @@ -14,7 +22,7 @@ Under no circumstances will we be liable for any loss or damage incurred as a re ## User Responsibility -The user assumes all responsibility and risk for the use of this Chatbot. It is the user's responsibility to evaluate the accuracy, completeness, or usefulness of any information, opinion, or content available through the Chatbot service. +The user assumes all responsibility and risk for the use of this Chatbot. It is the user's responsibility to evaluate the accuracy, completeness, or usefulness of any information, opinion, or content available through the Chatbot service. Users are reminded to carefully check with the original sources and to respect the respective licenses of any copyrighted materials. If you are the author of any material used by the Chatbot and wish to opt-out, please contact us via [this form](https://oeway.typeform.com/to/K3j2tJt7). ## Third-Party Links @@ -25,6 +33,7 @@ The Chatbot may provide links to external websites or resources for your conveni User interactions with the Chatbot may be stored for analysis and improvement of the service. All data will be handled in accordance with our Privacy Policy. ## Privacy Policy + The personal data you may provide will be used to disseminate information pertaining to the execution of the Horizon Europe Funded AI4Life project (Grant number: 101057970). In accordance with the Grant Agreement, your data will be retained during the project and deleted when it has ended as soon as the retention period established by the EC is over. If you would like to update or delete your data during the course of the project, please contact us using [this form](https://oeway.typeform.com/to/K3j2tJt7?typeform-source=bioimage.io). ## Modifications diff --git a/docs/README.md b/docs/README.md index 2a07ec6..5240039 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,8 +1,6 @@ # 🦒 BioImage.IO Chatbot 🤖 -**📣New Preprint: [![arXiv](https://img.shields.io/badge/arXiv-2310.18351-red.svg)](https://arxiv.org/abs/2310.18351) 10.5281/zenodo.10032228** - -**📚 Documentation: https://bioimage-io.github.io/bioimageio-chatbot/** +**📣 Publication on Nature Methods: https://www.nature.com/articles/s41592-024-02370-y ** **👇 Want to Try the Chatbot? [Visit here!](https://bioimage.io/chat)** @@ -102,16 +100,10 @@ To reproduce the use cases described in [Figure 2](https://docs.google.com/drawi ## Cite Us -If you use the BioImage.IO Chatbot in your research, please cite us: 10.5281/zenodo.10032228 - - -``` -Lei, W., Fuster-Barceló, C., Muñoz-Barrutia, A., & Ouyang, W. (2023). 🦒BioImage.IO Chatbot: A Personalized Assistant for BioImage Analysis Augmented by Community Knowledge Base (0.1.0). Zenodo. https://doi.org/10.5281/zenodo.10032228 -``` +If you use the BioImage.IO Chatbot in your research, please cite us: -You can also reference our preprint available on arXiv: [![arXiv](https://img.shields.io/badge/arXiv-2310.18351-red.svg)](https://arxiv.org/abs/2310.18351) ``` -Lei, W., Fuster-Barceló, C., Muñoz-Barrutia, A., & Ouyang, W. (2023). 🦒BioImage.IO Chatbot: A Personalized Assistant for BioImage Analysis Augmented by Community Knowledge Base. arXiv. https://arxiv.org/abs/2310.18351 +Lei, W., Fuster-Barceló, C., Reder, G. et al. BioImage.IO Chatbot: a community-driven AI assistant for integrative computational bioimaging. Nat Methods 21, 1368–1370 (2024). https://doi.org/10.1038/s41592-024-02370-y ``` ## Acknowledgements @@ -136,3 +128,4 @@ We would also like to thank the open-source community for their ongoing support Thank you for supporting the BioImage.IO project and contributing to the advancement of bioimage analysis! +See the full [Disclaimer for BioImage.IO Chatbot](./DISCLAIMER.md). From 86d2176a7475f5db24a91c860f1c6e17e7a181d8 Mon Sep 17 00:00:00 2001 From: Wei Ouyang Date: Sat, 10 Aug 2024 14:06:25 -0700 Subject: [PATCH 05/10] Update acknowledgements --- docs/DISCLAIMER.md | 2 +- docs/README.md | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/DISCLAIMER.md b/docs/DISCLAIMER.md index f9e3fa9..c9bb9b7 100644 --- a/docs/DISCLAIMER.md +++ b/docs/DISCLAIMER.md @@ -2,7 +2,7 @@ ## Research Purpose and Use of Copyrighted Material -The BioImage.IO Chatbot ("Chatbot") is part of a research project focused on Text and Data Mining (TDM) to support advancements in bioimage analysis. The primary purpose of this Chatbot is to assist users in navigating resources, tools, and workflows related to bioimage analysis for research and educational purposes. In compliance with the European Union's copyright exception on TDM as outlined in [Directive (EU) 2019/790](https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX%3A32019L0790), the Chatbot utilizes copyrighted materials to which we have lawful access. These materials are used exclusively for non-commercial research purposes. +The BioImage.IO Chatbot ("Chatbot") is part of a research project focused on Text and Data Mining (TDM) to support advancements in bioimage analysis. The primary purpose of this Chatbot is to assist users in navigating resources, tools, and workflows related to bioimage analysis for research purposes. In compliance with the European Union's copyright exception on TDM as outlined in [Directive (EU) 2019/790](https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX%3A32019L0790), the Chatbot utilizes copyrighted materials to which we have lawful access. These materials are used exclusively for non-commercial research purposes. ## Evaluation-Only Use of Source Code and Live Demo diff --git a/docs/README.md b/docs/README.md index 5240039..fe61850 100644 --- a/docs/README.md +++ b/docs/README.md @@ -108,6 +108,8 @@ Lei, W., Fuster-Barceló, C., Reder, G. et al. BioImage.IO Chatbot: a community- ## Acknowledgements +The BioImage.IO Chatbot is greatly enriched by the valuable resources contributed by the global bioimage analysis community. We extend our deepest gratitude to all authors and contributors listed in the [knowledge base manifest](https://github.com/bioimage-io/bioimageio-chatbot/blob/main/knowledge-base-manifest.yaml), especially the original authors of the materials integrated into our extensions. Their work has significantly enhanced the capabilities of this chatbot, providing users with high-quality information and tools. + We thank [AI4Life consortium](https://ai4life.eurobioimaging.eu/) for its crucial support in the development of the BioImage.IO Chatbot. ![AI4Life](https://ai4life.eurobioimaging.eu/wp-content/uploads/2022/09/AI4Life-logo_giraffe-nodes-2048x946.png) @@ -116,7 +118,6 @@ AI4Life has received funding from the European Union’s Horizon Europe research ## Disclaimer -The BioImage.IO Chatbot is greatly enriched by the valuable resources contributed by the global bioimage analysis community. We extend our deepest gratitude to all contributors, especially the original authors of the materials integrated into our extensions. Their work has significantly enhanced the capabilities of this chatbot, providing users with high-quality information and tools. These resources are primarily utilized for research purposes in compliance with the European Union's copyright exception on Text and Data Mining (TDM) as outlined in [Directive (EU) 2019/790](https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX%3A32019L0790). From ee09b48cbd2b2d5a3483299c4b67b62b722f5980 Mon Sep 17 00:00:00 2001 From: Wei Ouyang Date: Sat, 10 Aug 2024 14:12:45 -0700 Subject: [PATCH 06/10] Update acknowledgements --- docs/README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/README.md b/docs/README.md index fe61850..53a99fa 100644 --- a/docs/README.md +++ b/docs/README.md @@ -110,12 +110,16 @@ Lei, W., Fuster-Barceló, C., Reder, G. et al. BioImage.IO Chatbot: a community- The BioImage.IO Chatbot is greatly enriched by the valuable resources contributed by the global bioimage analysis community. We extend our deepest gratitude to all authors and contributors listed in the [knowledge base manifest](https://github.com/bioimage-io/bioimageio-chatbot/blob/main/knowledge-base-manifest.yaml), especially the original authors of the materials integrated into our extensions. Their work has significantly enhanced the capabilities of this chatbot, providing users with high-quality information and tools. +We would also like to thank the open-source community for their ongoing support and innovation, which continuously drives the development and improvement of the BioImage.IO platform. + We thank [AI4Life consortium](https://ai4life.eurobioimaging.eu/) for its crucial support in the development of the BioImage.IO Chatbot. ![AI4Life](https://ai4life.eurobioimaging.eu/wp-content/uploads/2022/09/AI4Life-logo_giraffe-nodes-2048x946.png) AI4Life has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement number 101057970. Views and opinions expressed are, however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. +Thank you for supporting the BioImage.IO project and contributing to the advancement of bioimage analysis! + ## Disclaimer @@ -125,8 +129,4 @@ The full list of sources and resources used by the BioImage.IO Chatbot can be fo If you are an author of any material used within the BioImage.IO Chatbot and wish to have your content removed, please contact us directly. We are committed to respecting the rights of all contributors and will promptly address your request. -We would also like to thank the open-source community for their ongoing support and innovation, which continuously drives the development and improvement of the BioImage.IO platform. - -Thank you for supporting the BioImage.IO project and contributing to the advancement of bioimage analysis! - See the full [Disclaimer for BioImage.IO Chatbot](./DISCLAIMER.md). From 12dafccd82ea68f0ba606509ca2501b8ed9942aa Mon Sep 17 00:00:00 2001 From: alalulu8668 Date: Sun, 11 Aug 2024 21:19:34 +0200 Subject: [PATCH 07/10] add infor for community source --- knowledge-base-manifest.yaml | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/knowledge-base-manifest.yaml b/knowledge-base-manifest.yaml index 71953a7..c8074cc 100644 --- a/knowledge-base-manifest.yaml +++ b/knowledge-base-manifest.yaml @@ -8,6 +8,10 @@ collections: 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" + reference: "https://www.ilastik.org/documentation/" format: markdown - name: BioImage.IO id: bioimage.io @@ -15,6 +19,10 @@ collections: 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" + reference: "https://bioimage.io/docs/" format: markdown - name: imagej.net id: imagej.net @@ -22,6 +30,10 @@ collections: 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" + reference: "https://github.com/imagej/imagej.github.io?tab=readme-ov-file" format: markdown - name: bio.tools id: bio.tools @@ -29,6 +41,10 @@ collections: 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" + reference: "https://biotools.readthedocs.io/en/latest/index.html" format: json - name: ImJoy id: imjoy @@ -36,6 +52,10 @@ collections: 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" + reference: "https://imjoy.io/docs/#/" format: markdown - name: deepImageJ id: deepimagej @@ -43,12 +63,24 @@ collections: directory: "." description: The ImageJ plugin to run deep-learning models base_url: https://deepimagej.github.io/ + authors: + - name: DeepImageJ Team + license: "BSD 2-Clause" + 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" + reference: "https://github.com/scikit-image/scikit-image?tab=readme-ov-file" format: pdf - name: napari id: napari @@ -56,6 +88,10 @@ collections: 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" + reference: "https://github.com/napari/napari?tab=readme-ov-file" format: markdown - name: Introduction to Bioimage Analysis id: book-itba From ad717c9cf863b7f7215308c1ce4fc4b887a522e4 Mon Sep 17 00:00:00 2001 From: alalulu8668 Date: Wed, 14 Aug 2024 02:12:29 +0200 Subject: [PATCH 08/10] add reference link to the response. add info in more_details. --- bioimageio_chatbot/chatbot.py | 21 ++++ .../chatbot_extensions/docs_extension.py | 13 +- bioimageio_chatbot/static/index.html | 112 ++++++++++++------ knowledge-base-manifest.yaml | 42 +++---- 4 files changed, 125 insertions(+), 63 deletions(-) diff --git a/bioimageio_chatbot/chatbot.py b/bioimageio_chatbot/chatbot.py index 3995d2f..6447c1a 100644 --- a/bioimageio_chatbot/chatbot.py +++ b/bioimageio_chatbot/chatbot.py @@ -152,7 +152,28 @@ class ThoughtsSchema(BaseModel): tool_usage_prompt=tool_usage_prompt, ) result_steps = metadata["steps"] + + # Create a map to store the mapping of result step names to their corresponding info + info_map = {} + # Iterate through each extension in the dictionary + for ext_id, ext in extensions_by_id.items(): + # Iterate through the info dictionary of each extension + for tool_key, tool_info in ext.info.items(): + # remove all special characters and convert to lowercase, and add `ext_id` to the beginning + step_name = f"{ext_id}-{tool_key}".replace(" ", "").replace("-", "").replace("_","").lower() + # Map the step name to the tool info + info_map[step_name] = tool_info + for idx, step_list in enumerate(result_steps): + for step in step_list: + # Get the step name + step_name = step['name'].lower() + # Get the corresponding info for the step + step_info = info_map.get(step_name) + if step_info: + # Add the info to the step details + step["info"] = step_info + steps.append( ResponseStep( name=f"step-{idx}", details={"details": convert_to_dict(step_list)} diff --git a/bioimageio_chatbot/chatbot_extensions/docs_extension.py b/bioimageio_chatbot/chatbot_extensions/docs_extension.py index 0c2f1f1..d30a7e1 100644 --- a/bioimageio_chatbot/chatbot_extensions/docs_extension.py +++ b/bioimageio_chatbot/chatbot_extensions/docs_extension.py @@ -112,13 +112,18 @@ async def run_extension( channel_id = collection["id"] base_url = collection.get("base_url") + reference = collection.get("reference") if base_url: base_url_prompt = f" The documentation is available at {base_url}." else: base_url_prompt = "" - + + if reference: + reference_prompt = f" The reference is available at {reference}." + else: + reference_prompt = "" run_extension.__name__ = "Search" + title_case(channel_id) - run_extension.__doc__ = f"""Searching documentation for {channel_id}: {collection['description']}.{base_url_prompt}""" + run_extension.__doc__ = f"""Searching documentation for {channel_id}: {collection['description']}.{base_url_prompt}. {reference_prompt}""" return schema_tool(run_extension) INFO_KEYS = ["name","description", "authors", "license", "reference"] @@ -162,7 +167,7 @@ def get_extension(): sinfo1 = ChatbotExtension( id="docs", name="Search BioImage Docs", - description="Search information in the documents of the bioimage.io knowledge base. Provide a list of keywords to search information in the documents. Returns a list of relevant documents.", + description="Search information in the documents of the bioimage.io knowledge base. Provide a list of keywords to search information in the documents. Returns a list of relevant documents. Ensure that the reference to the document is ALWAYS included!", tools=docs_tools, info=docs_info ) @@ -170,7 +175,7 @@ def get_extension(): sinfo2 = ChatbotExtension( id="books", name="Search BioImage Books", - description="Search information in BioImage books. Provide a list of keywords to search information in the books. Returns a list of relevant documents.", + description="Search information in BioImage books. Provide a list of keywords to search information in the books. Returns a list of relevant documents. Ensure that the reference to the book is ALWAYS included!", tools=books_tools, info=books_info ) diff --git a/bioimageio_chatbot/static/index.html b/bioimageio_chatbot/static/index.html index 3b55f59..94d26cd 100644 --- a/bioimageio_chatbot/static/index.html +++ b/bioimageio_chatbot/static/index.html @@ -1910,49 +1910,85 @@

Welcome to BioImage.IO Chatbot

} const steps = response.steps; let message = response.text && marked(response.text, { renderer: renderer }) || ""; - if (steps && steps.length > 0) { - let details = "
🔍More Details\n\n" - for (let step of steps) { - details += `## ${step.name}\n\n`; - - if (step.details.details) { - for (let detail of step.details.details) { - details += `-----\n### Tool Call: \`${detail.name}\`\n\n`; - details += "#### Arguments:\n\n"; - if (detail.args && detail.args.length > 0) { - for (let arg of detail.args) { - const argValue = JSON.stringify(arg); - details += `\`\`\`\n${argValue}\n\`\`\`\n\n`; - } - details += "\n\n"; - } - if (detail.kwargs) { - for (let kwarg in detail.kwargs) { - const kwargValue = typeof detail.kwargs[kwarg] === 'string' ? detail.kwargs[kwarg] : JSON.stringify(detail.kwargs[kwarg], null, 2); - if(kwargValue.includes('\n')) - details += `**- \`${kwarg}\`**:\n\n\`\`\`\n${kwargValue}\n\`\`\`\n\n`; - else - details += `**- \`${kwarg}\`**: \`${kwargValue}\`\n\n`; - } - details += "\n\n"; - } - - if(detail.result){ - const result = typeof detail.result === 'string' ? detail.result : JSON.stringify(detail.result, null, 2); - if(result.includes('\n')) - details += `#### Result:\n\n\`\`\`\n${result}\n\`\`\`\n\n`; - else - details += `#### Result: \`${result}\`\n\n`; + if (steps && steps.length > 0) { + let details = "
🔍More Details\n\n"; + + for (let step of steps) { + details += `## ${step.name}\n\n`; + + if (step.details.details) { + for (let detail of step.details.details) { + details += `-----\n### Tool Call: \`${detail.name}\`\n\n`; + details += "#### Arguments:\n\n"; + + if (detail.args && detail.args.length > 0) { + for (let arg of detail.args) { + const argValue = JSON.stringify(arg); + details += `\`\`\`\n${argValue}\n\`\`\`\n\n`; + } + details += "\n\n"; + } + + if (detail.kwargs) { + for (let kwarg in detail.kwargs) { + const kwargValue = typeof detail.kwargs[kwarg] === 'string' ? detail.kwargs[kwarg] : JSON.stringify(detail.kwargs[kwarg], null, 2); + if (kwargValue.includes('\n')) { + details += `**- \`${kwarg}\`**:\n\n\`\`\`\n${kwargValue}\n\`\`\`\n\n`; + } else { + details += `**- \`${kwarg}\`**: \`${kwargValue}\`\n\n`; + } + } + details += "\n\n"; + } + + if (detail.result) { + const result = typeof detail.result === 'string' ? detail.result : JSON.stringify(detail.result, null, 2); + if (result.includes('\n')) { + details += `#### Result:\n\n\`\`\`\n${result}\n\`\`\`\n\n`; + } else { + details += `#### Result: \`${result}\`\n\n`; + } + } + + // Check for the existence of 'info' and display it if available + if (detail.info) { + const tool = detail.info; + details += `----\n> **Source:**\n>\n`; // Quoted title "Source" + details += `> **📚 Source Name**: ${tool.name}\n>\n`; // Quoted source name with book emoji + + details += `> **📝 Description**: ${tool.description}\n>\n`; // Quoted description + + if (tool.authors && tool.authors.length > 0) { + details += `> **👥 Authors**:\n>`; + for (const author of tool.authors) { + details += `\n> - ${author.name}, *${author.organization}*`; + } + details += `\n>\n`; // Ensure spacing after authors + } + + if (tool.license) { + details += `> **📜 License**: ${tool.license}\n>\n`; + } + + if (tool.reference) { + details += `> **🔗 [Reference](${tool.reference})**: ${tool.reference}\n>\n`; + } + details += `----\n`; // Close the quoted section + } + + + } } - } } - } - details += "\n\n
"; - details = marked(details, { renderer: renderer }); - message = message + details; + + details += "\n\n
"; + details = marked(details, { renderer: renderer }); + message = message + details; } + $(`#content-${currentMessageId}`).html(message); + } catch (e) { diff --git a/knowledge-base-manifest.yaml b/knowledge-base-manifest.yaml index c8074cc..685a1b5 100644 --- a/knowledge-base-manifest.yaml +++ b/knowledge-base-manifest.yaml @@ -10,7 +10,7 @@ collections: base_url: https://www.ilastik.org/documentation/ authors: - name: ilastik Team - license: "GPLv2" + license: "[GPLv2](https://www.ilastik.org/license)" reference: "https://www.ilastik.org/documentation/" format: markdown - name: BioImage.IO @@ -21,7 +21,7 @@ collections: base_url: https://bioimage.io/docs/ authors: - name: BioImage.IO Team - license: "MIT License" + 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 @@ -32,7 +32,7 @@ collections: base_url: https://imagej.net authors: - name: ImageJ Team - license: "Creative Commons Attribution 3.0 Unported" + 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 @@ -43,7 +43,7 @@ collections: base_url: https://bio.tools authors: - name: bio.tools Team - license: "CC BY 4.0" + 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 @@ -54,7 +54,7 @@ collections: base_url: https://imjoy.io/docs/#/ authors: - name: ImJoy Team - license: "MIT License" + license: "[MIT License](https://imjoy.io/docs/#/?id=license)" reference: "https://imjoy.io/docs/#/" format: markdown - name: deepImageJ @@ -65,7 +65,7 @@ collections: base_url: https://deepimagej.github.io/ authors: - name: DeepImageJ Team - license: "BSD 2-Clause" + 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 @@ -79,7 +79,7 @@ collections: - name: Juan Nunez-Iglesias organization: Monash University - name: et al. - license: "BSD 3-Clause" + 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 @@ -90,7 +90,7 @@ collections: base_url: https://napari.org/stable/ authors: - name: napari Team - license: "BSD 3-Clause" + 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 @@ -102,7 +102,7 @@ collections: authors: - name: Pete Bankhead organization: University of Edinburgh - license: "CC BY 4.0" + 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 @@ -117,7 +117,7 @@ collections: organization: Tel Aviv University - name: Dinggang Shen organization: ShanghaiTech University - license: "All rights reserved" + 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 @@ -128,7 +128,7 @@ collections: authors: - name: Nikon organization: Nikon - license: "All rights reserved" + 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 @@ -140,19 +140,19 @@ collections: - name: Kota Miura organization: Nikon Imaging Center, Heidelberg reference: "https://analyticalscience.wiley.com/content/article-do/bioimage-data-analysis" - license: "All rights reserved" + 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.rsna.org/-/media/Files/RSNA/Education/RSNA-Press/Deep-Learning-in-Medical-Imaging.pdf + 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" + 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 @@ -166,7 +166,7 @@ collections: - name: Aasa Feragen organization: Technical University of Denmark - name: et al. - license: "arXiv.org perpetual, non-exclusive license 1.0" + 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 @@ -182,7 +182,7 @@ collections: - name: Lei Tian organization: Boston University - name: et al. - license: "arXiv.org perpetual, non-exclusive license 1.0" + 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 @@ -199,7 +199,7 @@ collections: organization: Instituto Gulbenkian de Ciência, Oeiras, Portugal - name: Ricardo Henriques organization: Instituto Gulbenkian de Ciência, Oeiras, Portugal - license: "All rights reserved" + 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 @@ -215,7 +215,7 @@ collections: - name: Luis Ibáñez organization: Google LLC - name: Insight Software Consortium - license: "Apache 2.0" + 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 @@ -231,7 +231,7 @@ collections: - name: Luis Ibáñez organization: Google LLC - name: Insight Software Consortium - license: "Apache 2.0" + 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 @@ -242,7 +242,7 @@ collections: base_url: https://docs.itk.org authors: - name: Insight Software Consortium - license: "Apache 2.0" + 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 @@ -253,7 +253,7 @@ collections: base_url: https://wasm.itk.org authors: - name: Insight Software Consortium - license: "Apache 2.0" + 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: From d33593174a78802cfbf062279ea70021a0cd8d9d Mon Sep 17 00:00:00 2001 From: Wei Ouyang Date: Wed, 14 Aug 2024 13:11:34 -0700 Subject: [PATCH 09/10] Fix bioimage data analysis book --- knowledge-base-manifest.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/knowledge-base-manifest.yaml b/knowledge-base-manifest.yaml index 685a1b5..251b9f1 100644 --- a/knowledge-base-manifest.yaml +++ b/knowledge-base-manifest.yaml @@ -134,10 +134,10 @@ collections: - name: BioImage Data Analysis id: book-bda source: https://raw.githubusercontent.com/oeway/hypha-knowledge-base/gh-pages/bioimagedataanalysis-compressed.pdf - description: "A book written by Kota Miura about bioimage data analysis" + description: "A book about bioimage data analysis" base_url: https://analyticalscience.wiley.com/content/article-do/bioimage-data-analysis authors: - - name: Kota Miura + - 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]" From af0c69aaca6323120250c6168375956d366a15e8 Mon Sep 17 00:00:00 2001 From: Wei Ouyang Date: Wed, 14 Aug 2024 13:15:19 -0700 Subject: [PATCH 10/10] bump version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c3b47e9..5fec199 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ requires = ["setuptools", "wheel"] [project] name = "bioimageio-chatbot" -version = "0.2.9" +version = "0.2.10" readme = "README.md" description = "Your Personal Assistant in Computational BioImaging." dependencies = [