diff --git a/content/community/sig/image-analysis/FAIR-wf-postcard.png b/content/community/sig/image-analysis/FAIR-wf-postcard.png new file mode 100644 index 0000000000..00aa7a0f24 Binary files /dev/null and b/content/community/sig/image-analysis/FAIR-wf-postcard.png differ diff --git a/content/community/sig/image-analysis/FAIR-wf-poster.png b/content/community/sig/image-analysis/FAIR-wf-poster.png new file mode 100644 index 0000000000..68a65b269a Binary files /dev/null and b/content/community/sig/image-analysis/FAIR-wf-poster.png differ diff --git a/content/community/sig/image-analysis/image-analysis-interface.png b/content/community/sig/image-analysis/image-analysis-interface.png new file mode 100644 index 0000000000..9182986a08 Binary files /dev/null and b/content/community/sig/image-analysis/image-analysis-interface.png differ diff --git a/content/community/sig/image-analysis/index.md b/content/community/sig/image-analysis/index.md new file mode 100644 index 0000000000..d21444b781 --- /dev/null +++ b/content/community/sig/image-analysis/index.md @@ -0,0 +1,154 @@ +--- +description: "If you need to extract quantitative information from images and want to make your workflows reusable, this community is for you." +autotoc: true +title: "Image Analysis Community in Galaxy" +--- + + + + +Welcome to the Image Analysis Community in Galaxy! + +Image analysis bridges multiple disciplines, and this community gathers researchers and developers from diverse scientific fields to share knowledge, tools, and workflows. + +## Community goals + +Our primary goals are to: +* **Coordinate efforts** across the Galaxy ecosystem to reduce redundancy in tools, workflows, and training. +* **Share our work** — from within and outside Galaxy—to showcase our advancements. +* **Support each other** through knowledge-sharing, troubleshooting, and collaboration. + +Additionally, we strive to: +* **Develop and maintain** image analysis tools within Galaxy. +* **Implement FAIR principles** to make workflows reproducible and reusable. +* **Expand documentation** and **training resources** for accessible learning and skill-building. + + +## Who we are + +We are a diverse group of users, developers, trainers, and image data enthusiasts, collaborating to expand Galaxy’s image analysis capabilities, bringing the latest tools, feedback, and beyond. + +- **Developers**: Are you building image analysis tools in Galaxy, or thinking of starting a project here? Do you need users, testers, or just want to make sure you’re not duplicating tools that already exist? Join us to connect, share ideas, and get support for your development journey! + +- **Users**: Do you use Galaxy’s image analysis tools for bioimaging, Earth observation, or other fields? Have feedback for us, or interested in testing new resources? Perhaps you have ideas or requests for new tools — your input can help shape future developments! + +- **Trainers**: Are you using Galaxy to train others in image analysis? If you have suggestions or specific needs to better support your trainees, we'd love to hear from you. Your insights are invaluable in helping us create better learning experiences and share data image analysis knowledge. + +# Getting started: GTN tutorials + +To dive into Galaxy, the [Galaxy Training Network (GTN)](https://training.galaxyproject.org) offers a wealth of tutorials for beginners and experts alike. These tutorials cover basic and advanced workflows, guiding you through analyses step-by-step. They also include a curated selection of workflows to help you gain hands-on experience in Galaxy. + + + +# What is available? + +## Image analysis tools + +The Galaxy ToolShed offers a variety of tools for image data analysis, freely available for installation on any Galaxy server. Our community maintains a curated list of available tools to keep users informed and up-to-date. + + + +*Are we missing some tools? [Reach out to us](https://matrix.to/#/#galaxyproject_imaging:matrix.org) to keep the list comprehensive.* + +## Interactive tools + +Image analysis often involves hands-on interaction, and Galaxy offers resources that make this possible. Check out our interactive tools to experience Galaxy's potential beyond traditional workflows. + +![Napari](/images/galaxy-napari.png) + +## Visualizations + +The **[zarr](https://zarr.dev/)** format is becoming a standard for storing large image data. With various adaptations like [OME-Zarr](https://ome-zarr.readthedocs.io/en/stable/) and [GEOZarr](https://github.com/zarr-developers/geozarr-spec), this interoperable format enhances data reusability across disciplines. Our community supports zarr-based visualization through tools like vizarr, helping bring this dream of cross-discipline interoperability to life. + + + +## A dedicated Galaxy interface + +Our dedicated interface for image data analysis—[imaging.usegalaxy.eu](https://imaging.usegalaxy.eu)—provides a comprehensive suite of tools and workflows tailored specifically for imaging scientists. + +Image Analysis dedicated interface in Galaxy + + +# How to get involved? + +If you're interested in image analysis (within or outside Galaxy) and want to help ensure our tools represent the best, up-to-date practices, your feedback is needed! We’re constantly looking for ways to improve, whether in scientific fields already supported by Galaxy or in exploring new applications. + +If you're **passionate about shaping the future of image analysis in Galaxy** and want to help build a strong, collaborative, and supportive community, **you're in the right place!** + +## Communication channels + +Our community connects via our dedicated [Matrix channel](https://matrix.to/#/#galaxyproject_imaging:matrix.org). + +## Online community meetings + +FAIR Workflows Expert Group postcard + +We organize regular meetups as part of the Euro-BioImaging Expert Group "FAIR Image Data Workflows," chaired by Anne Fouilloux and Beatriz Serrano-Solano. + +- **Frequency**: Monthly +- **Duration**: 1 hour +- **Time**: 3rd Wednesday of the month at 4 pm CET +- **Meeting Agenda**: Updates from the community (e.g., upcoming events), relevant talks or case studies, and coordination for activities such as grant writing, paper development, and event planning. View our [open agenda and notes here](https://docs.google.com/document/d/1eWyj5IJVW4qeLKcz2SybHbf0Kx6K3Njvirl6ql-f1Fo/edit?tab=t.0#heading=h.wvq01nlj8eqb). + +## In-person meetings and conferences + +In-person meetups are also part of our community engagement. We recently participated in BioHackathon 2023 and 2024, where we collaborated on new projects and shared [preprints](https://osf.io/preprints/biohackrxiv/w8dsz). + +FAIR Workflows Expert Group postcard + +Poster available in [Zenodo](https://zenodo.org/records/13847465). + +## Community calendar + + + + +# Acknowledgments + +Our community's success is made possible through partnerships and collaborations. We thank our partners for their support. + +## Partner projects + +Community members actively pursue funding opportunities and contribute to various projects, such as: + +| Project Name | Description | Community Members Involved | Funding Period | +|-------------------|-------------------------------------------------------------------------------------------------------|-----------------------------------------------------------|----------------| +| [**NFDI4BIOIMAGE**](https://nfdi4bioimage.de/) | NFDI4BIOIMAGE is working on solutions that enable researchers in bioimaging to handle, store, share, and reuse bioimaging data. | Riccardo Massei, Bjoern Gruening, Yi Sun | 2022 - 2027 | +| [**OSCARS**](https://oscars-project.eu/) | Creating reusable workflows for diverse disciplines like microscopy, astrophysics, and environmental sciences | Beatriz Serrano-Solano, Anne Fouilloux, Matus Kalas | 2025 - 2027 | + + + + + + + + + + +
+Euro-BioImaging + +Simula + +BMCV + +UFZ + +EDAM + +NFDI4BIOIMAGE + +OSCARS +
\ No newline at end of file diff --git a/content/community/sig/image-analysis/vizarr-visualization.mp4 b/content/community/sig/image-analysis/vizarr-visualization.mp4 new file mode 100644 index 0000000000..7ff3005551 Binary files /dev/null and b/content/community/sig/image-analysis/vizarr-visualization.mp4 differ diff --git a/content/community/sig/index.md b/content/community/sig/index.md index dd846b09dd..aff4c09343 100644 --- a/content/community/sig/index.md +++ b/content/community/sig/index.md @@ -203,6 +203,19 @@ The Single cell and sPatial Omics Community (🖖🏾SPOC) unites tool developer * [](https://singlecell.usegalaxy.eu) + +
+ +
Image Analysis
+ + +This community gathers image analysis enthusiasts across different scientific disciplines. + +* [[m]   Matrix](https://matrix.to/#/#imaging:matrix.org) +* [   GTN](https://training.galaxyproject.org/training-material/topics/imaging/) +* [](https://imaging.usegalaxy.eu) +
+ diff --git a/content/news/2024-02-26-napari-available/galaxy-napari.png b/content/images/galaxy-napari.png similarity index 100% rename from content/news/2024-02-26-napari-available/galaxy-napari.png rename to content/images/galaxy-napari.png diff --git a/content/images/logos/UFZ-logo.png b/content/images/logos/UFZ-logo.png new file mode 100644 index 0000000000..5ed5bc2214 Binary files /dev/null and b/content/images/logos/UFZ-logo.png differ diff --git a/content/images/logos/edam-bioimaging-logo.png b/content/images/logos/edam-bioimaging-logo.png new file mode 100644 index 0000000000..e41ae6a05c Binary files /dev/null and b/content/images/logos/edam-bioimaging-logo.png differ diff --git a/content/images/logos/logo_BMCV.png b/content/images/logos/logo_BMCV.png new file mode 100644 index 0000000000..6a3a656aba Binary files /dev/null and b/content/images/logos/logo_BMCV.png differ diff --git a/content/images/logos/simula-logo.png b/content/images/logos/simula-logo.png new file mode 100644 index 0000000000..52f907df14 Binary files /dev/null and b/content/images/logos/simula-logo.png differ diff --git a/content/news/2024-02-26-napari-available/index.md b/content/news/2024-02-26-napari-available/index.md index f89fd97cd4..8ecabfb3f5 100644 --- a/content/news/2024-02-26-napari-available/index.md +++ b/content/news/2024-02-26-napari-available/index.md @@ -22,7 +22,7 @@ Napari provides a dynamic platform for visualizing and interacting with 2D, 3D, To use Napari in Galaxy, first you need to create an account in Galaxy and log in with your credentials. You can access Napari from [here](https://usegalaxy.eu/root?tool_id=interactive_tool_napari) and specify images from your history that you want to visualize using Napari, then press the _Run Tool_ button to launch a Napari instance. When the graphical user interface of Napari is ready, an 'Open' link will be displayed at the top of the Galaxy central panel (see screenshot below). -![Napari](./galaxy-napari.png) +![Napari](/images/galaxy-napari.png) We are still working on integrating more plugins into the Napari interactive tool in Galaxy.