Small fix (#381)

Co-authored-by: Wei Ouyang <[email protected]>

docs/README.md

@@ -1,27 +1,22 @@
-# BioImage Model Zoo: Advanced AI models in one-click
+# Welcome to BioImage.IO Documentation
 
-The Bioimage Model Zoo is a community-driven AI model repository. The aim is to facilitate the adoption of AI methods among the bioimaging community by providing easy access to pretrained AI models. By establishing a common Model Resource Description File Specification, the model zoo serves as a distribution point for deep learning models trained to perform bioimage analysis tasks.
+Welcome to the official BioImage.IO documentation. Here, you'll find comprehensive resources designed to support your journey through the fascinating world of bioimaging. Our documentation is structured to provide easy access to all the information you need, whether you're just starting out or looking to deepen your expertise.
 
-Several founding partners including ilastik, ImJoy, Fiji, deepImageJ and ZeroCostDL4Mic are involved in the creation of the model zool and we welcome more community partners to join the efforts. Our vision is to define a common standard which would allow all models in the model zoo to be compatible with community partner tools. Such compatibility will ensure that the models in the model zoo can be interoperable between different tools and truly be used by non-computational biologists through user-friendly interface. 
+## Quick Navigation
 
-In addition to the Model Resource Description File Specification, we aim to make cutting-edge AI technology accessible to our users by providing detailed model descriptions, tagging, searching and automatic testing of all submitted models. Models can be directly executed from the site with users' own data samples, and linked to its training data and Jupyter/Colab Notebooks.
+- **[Getting Started](/getting_started/README.md)**: Introduction to the BioImage Model Zoo ecosystem, who are we and how can you be part of it.
+- **[Guides](/guides/README.md)**: In-depth tutorials and guides regarding the BioImage Model Zoo as a user, contributor or Community Partner.
+- **[Tools and Resources](/tools_and_resources/README.md)**: Overview of the available tools and resources linked to the BioImage Model Zoo.
+- **[Help Desk](/help_desk/README.md)**: A bit lost? Check the help desk for more information, a glossary page and how to contact us!
+- **[Terms of Service](/terms_of_service.md)**: Usage policies and guidelines.
+- **[Code of Conduct](/CODE_OF_CONDUCT.md)**: The code of conduct for the ecosystem.
 
-The model zoo is open for contributions from the community partners and external individuals. You are welcome to submit models to the model zoo. We will do our best to ensure you have a smooth experience contributing your work which will of course remain in your IP with all necessary attributions. 
+## Explore and Discover
 
-<img src="./bioimage_description.png" align="center" width="1000"/>
+Dive into our documentation to explore the tools, resources, and support available to enhance your knowledge about the BioImage Model Zoo ecosystem. If you have any questions or need further assistance, our Help Desk is ready to assist you. Happy exploring!
 
-# Reference publication
+## Reference publication
 Wei Ouyang, Fynn Beuttenmueller, Estibaliz Gómez-de-Mariscal, Constantin Pape, Tom Burke, Carlos Garcia-López-de-Haro, Craig Russell, Lucía Moya-Sans, Cristina de-la-Torre-Gutiérrez, Deborah Schmidt, Dominik Kutra, Maksim Novikov, Martin Weigert, Uwe Schmidt, Peter Bankhead, Guillaume Jacquemet, Daniel Sage, Ricardo Henriques, Arrate Muñoz-Barrutia, Emma Lundberg, Florian Jug, Anna Kreshuk, **BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis**, bioRxiv 2022.06.07.495102, doi: [https://doi.org/10.1101/2022.06.07.495102](https://doi.org/10.1101/2022.06.07.495102)
 
 <img src="./bioimage-io-paper-figure-1.png" align="center" width="1000"/>
 
-# Glossary
-In the ever-evolving field of bioimage analysis, understanding the terminology is essential. Explore our glossary to familiarize yourself with key terms and concepts used throughout the BioImage Model Zoo project.
-
-| Term                                  | Definition                                                                                                                                                           |
-| ------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| **Community Partner**                 | Usually, a community partner is an organization, a company, a research group, or a software team (of one or more) that can consume and/or produce resources of the BioImage Model Zoo. Additionally, most partners continuously and openly contribute resources of their own. The founders community partners represent open source consumer software of [BioImage.IO](http://BioImage.IO/) (e.g. [ilastik](https://www.ilastik.org), [Fiji](https://imagej.net/software/fiji/), [deepImageJ](https://deepimagej.github.io), [ZeroCostDL4Mic](https://github.com/HenriquesLab/ZeroCostDL4Mic), [StarDist](https://github.com/stardist/stardist)). A Community Partner can either be a team behind a software which produces or consumes trained models compatible with the [BioImage.IO](http://bioimage.io/) spec or an organization, group, company or team (of one or more) who contributed and will keep contributing more models to BioImage Model Zoo. |
-| **Consumer**                          | Refers to an individual or user who engages with the project by utilizing the pre-existing models available on [BioImage.IO](http://bioimage.io/). Their primary role involves downloading these models and incorporating them into their workflow using compatible software or any specific manner that suits their needs. For example, a Life Scientist can be considered a consumer by accessing the[BioImage.io](http://bioimage.io/), selecting a Deep Learning model relevant to their research, and integrating it into their preferred software, such as deepImageJ or other compatible platforms. As a consumer, their focus lies in leveraging the existing models to enhance their bioimage analysis tasks, thereby benefiting from the diverse range of models provided by the BioImage Model Zoo. |
-| **Contributor**                       | A contributor can either be an individual person or a group, entity, or software. As an individual contributor, your primary objective is to actively contribute to the project by uploading models to BioImage Model Zoo. By doing so, you expand the range of available models, enriching the repository and fostering the growth of the bioimage analysis community. As a contributor, you play a crucial role in sharing your expertise and innovative models with the broader community, contributing to advancements in bioimage analysis. Similarly, a software contributor refers to a software application or system that actively participates in the project by uploading models to [BioImage.IO](http://bioimage.io/). These software contributors enhance the available models by providing new and diverse solutions, further expanding the capabilities of the BioImage Model Zoo. Whether you contribute as an individual or a software entity, your active involvement in uploading models to [BioImage.IO](http://bioimage.io/) is instrumental in supporting the project's objectives. By sharing your models, you contribute to the collective knowledge and empower researchers in the bioimage analysis field. |
-| **Consumer Software**                 | A consumer software refers to any software application or tool that utilizes the models from the BioImage Model Zoo repository. Consumer software is designed to interact with and make use of the pretrained AI models available in the BioImage Model Zoo. A consumer software is any software application or tool that utilize pretrained AI models for bioimage analysis tasks, either through integration, execution, or interaction with the models available in the BioImage Model Zoo. |
-| **Model Resource Description File Specifications (RDF YAML)** | The Model Resource Description File (RDF) specifications refer to a set of guidelines that define the structure and content of a YAML file used to describe the AI models with pretrained weights in a standardized format. The model RDF serves as a metadata file that provides essential information about the model, its properties, and its intended use. The RDF file contains both mandatory and optional fields that capture relevant details about the model, such as its architecture, input/output formats, preprocessing steps, and performance metrics. By following the Model RDF specifications, developers and researchers can create consistent and interoperable descriptions of their AI models, allowing seamless integration and sharing within the [BioImage.IO](http://bioimage.io/) ecosystem. |

docs/_sidebar.md

@@ -1,29 +1,8 @@
 <!-- docs/_sidebar.md -->
-* [Overview](/)
-* [Getting Started](getting_started.md)
-* [User Guide](/user_guide/README.md)
-  - [Model download](/user_guide/tutorials.md)
-  - [Use-case 1: Stardist H&E nucleus segmentation](usecase1stardist)
-  - [Use-case 2: 3D U-Net for cell-segmentation in light microscopy](usecase2finetune)
-  - [Use-case 3: Classification, imjoy & python library usage](usecase3devtools)
-  - [Use-case 4: Domain adaptation for mitochondria segmentation in EM](usecase4domain)
-  - [Contribution of resources](bioimageio_collection_repo)
-* [BioEngine](/bioengine/README.md)
-  - [Tutorials](/bioengine/tutorials.md)
-* [Contribute Models](/contribute_models/README.md)
-  - [Model Specification](bioimageio_model_spec)
-  - [Upload models through Zenodo](/contribute_models/contribute_zenodo.md)
-* [Other contributions](/contribute_others/README.md)
-* [Resources for developers](/resources_developers/README.md)
-* [Consumer Software](/consumer_software/README.md)
-  - [Tutorials](/consumer_software/tutorials.md)
-  - [Model Runner](/consumer_software/model_runner.md)
-* [Community Partners](/community_partners/README.md)
-  - [How to join](/community_partners/how_to_join.md)
-  - [User Analytics](/community_partners/user_analytics.md)
-  - [BioImage.IO Partner Collection](/community_partners/partner_collection.md)
-* [FAQs](/faqs/README.md)
+* [Welcome](/README.md)
+* [Getting Started](/getting_started/README.md)
+* [Guides](/guides/README.md)
+* [Tools and Resources](/tools_and_resources/README.md)
+* [Help Desk](/help_desk/README.md)
 * [Terms of Service](/terms_of_service.md)
 * [Code of Conduct](/CODE_OF_CONDUCT.md)
-* [Governance](/bioimageio_steering.md)
-* [BioImageIO team guidelines](https://github.com/bioimage-io/bioimage.io/wiki)

docs/community_partners/README.md → docs/deprecated/community_partners/README.md

@@ -176,16 +176,3 @@ api.export(new ImJoyPlugin())
 ```
 
 
-| Tool Name      | WebPage                                   | Main Contact Person        | Institution                                 | Documentation                  |
-| -------------- | ----------------------------------------- | --------------------------- | ------------------------------------------- | ------------------------------ |
-| ZeroCostDL4Mic | [GitHub](https://github.com/HenriquesLab/ZeroCostDL4Mic) | Ricardo Henriques and Guillaume Jacquemet | [UTU](https://www.utu.fi/en) and [Abo Akademi](https://www.abo.fi)      | [Wiki](https://github.com/HenriquesLab/ZeroCostDL4Mic/wiki) |
-| DeepImageJ     | [Website](https://deepimagej.github.io)   | Arrate Muñoz Barrutia      | [UC3M](https://www.uc3m.es/home) and [EPFL](https://www.epfl.ch/en/) | [Wiki](https://github.com/deepimagej/deepimagej-plugin/wiki) |
-| ImJoy          | [Website](https://imjoy.io/#/)            | Wei Ouyang                 | [KTH](https://www.kth.se/en)              | [Docs](https://imjoy.io/docs/#/) |
-| Ilastik        | [Website](https://www.ilastik.org)       | Anna Kreshuk               | [EMBL](https://www.embl.org)             | [Docs](https://www.ilastik.org/documentation/index.html) |
-| icy            | [Website](https://icy.bioimageanalysis.org) | Jean-Christophe Olivo Marin | [IP](https://www.pasteur.fr/en)           | -                              |
-| Fiji           | [Website](https://fiji.sc)                | Florian Jug                | -                                           | [Docs](https://imagej.net/software/fiji/) |
-| HPA            | [Model Zoo](https://modelzoo.cellprofiling.org/#/) | Frederic Ballllosera Navarro           | [KTH](https://www.kth.se/en) and [Stanford](https://stanford.edu)             | -                              |
-| QuPath         | [Website](https://qupath.github.io)       | Pete Bankhead              | [UoE](https://www.ed.ac.uk)              | [Docs](https://qupath.readthedocs.io/en/stable/) |
-| StarDist       | [Website](https://stardist.net)           | Uwe Schmidt and Martin Weigert | -                                    | [GitHub](https://github.com/stardist/stardist) |
-
-

docs/community_partners/user_analytics.md → docs/deprecated/community_partners/user_analytics.md

@@ -2,7 +2,7 @@
 
 We provide the analytics service to help consumer software to keep track of their resource (including model, datasets etc.) downloads.
 
-## Report resource downloads
+### Report resource downloads
 
 To help us maintain the resource download statistics at BioImage.IO, please send a report to our analytics service when a resource item is downloaded.
 
@@ -22,7 +22,7 @@ In the above URL, you need to provide the following parameters:
  * `[CONSUMER VERSION]`: The software version for the consumer software.
 
 
-## Obtain resource usage statistics
+### Obtain resource usage statistics
 You can get the user statistics from via the HTTP API, for example:
  * To get the global statistics of the whole website: `https://bioimage.matomo.cloud/?module=API&method=Live.getCounters&idSite=1&lastMinutes=30&format=JSON&token_auth=anonymous`
  * To get the number of downloads: `https://bioimage.matomo.cloud/?module=API&method=Actions.getDownloads&idSite=1&period=year&date=2023-03-01&format=JSON&token_auth=anonymous`

docs/contribute_models/contribute_zenodo.md → docs/deprecated/contribute_models/contribute_zenodo.md

@@ -1,6 +1,6 @@
 # Uploading a Model to Zenodo for BioImage Model Zoo
 
-**Note:** This tutorial provides a temporary solution for uploading models to the BioImage Model Zoo via Zenodo while the upload feature on the BioImage.io website is being fixed.
+**Note:** This tutorial provides a temporary solution for uploading models to the BioImage Model Zoo via Zenodo while the upload feature on the BioImage.IO website is being fixed.
 
 ## Purpose
 This tutorial will guide you through the process of uploading a model to the BioImage Model Zoo community on Zenodo. The BioImage Model Zoo project aims to collect and share bioimage analysis models, and your contribution is valuable. Follow the steps below to upload your model.
@@ -12,7 +12,7 @@ This tutorial will guide you through the process of uploading a model to the Bio
    <img src="contribute_models/zenodo_upload_01.png" alt="Zenodo initial page" align="center" width="1000"/>
 
 2. On the right, close to your username, click the "New upload" button to begin the model upload process. Make sure that the repository is set as public. 
-The files in the BioImage.io zip have to be uploaded one-by-one (See the example in the image below). Note that you can drag & drop all together at once.
+The files in the BioImage.IO zip have to be uploaded one-by-one (See the example in the image below). Note that you can drag & drop all together at once.
    <!-- ![New upload](contribute_models/zenodo_upload_04.png) -->
    <img src="contribute_models/zenodo_upload_04.png" alt="New upload" align="center" width="1000"/>
 
@@ -28,4 +28,4 @@ The files in the BioImage.io zip have to be uploaded one-by-one (See the example
 
 
 ## Conclusion
-You've successfully uploaded your model to the BioImage Model Zoo community on Zenodo. Thank you for your contribution to the BioImage Model Zoo project. Remember that this is a temporary solution while the upload feature on the BioImage.io website is being fixed. We appreciate your patience and support!
+You've successfully uploaded your model to the BioImage Model Zoo community on Zenodo. Thank you for your contribution to the BioImage Model Zoo project. Remember that this is a temporary solution while the upload feature on the BioImage.IO website is being fixed. We appreciate your patience and support!