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bioimageio_collection_config.json
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bioimageio_collection_config.json
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{
"reviewers": [
{
"id": "github|15139589",
"name": "Fynn Beuttenmüller",
"affiliation": "European Molecular Biology Laboratory",
"orcid": "0000-0002-8567-6389",
"github_user": "fynnbe",
"email": "[email protected]"
},
{
"id": "github|478667",
"name": "Wei Ouyang",
"affiliation": "KTH Royal Institute of Technology",
"orcid": "0000-0002-0291-926X",
"github_user": "oeway",
"email": "[email protected]"
},
{
"id": "github|4263537",
"name": "Constantin Pape",
"affiliation": "University Goettingen",
"orcid": "0000-0001-6562-7187",
"github_user": "constantinpape",
"email": "[email protected]"
},
{
"id": "github|32868330",
"name": "Daniel Franco-Barranco",
"affiliation": "University of the Basque Country",
"orcid": "0000-0002-1109-110X",
"github_user": "danifranco",
"email": "[email protected]"
},
{
"id": "github|24434157",
"name": "Dominik Kutra",
"affiliation": "European Molecular Biology Laboratory",
"orcid": "0000-0003-4202-3908",
"github_user": "k-dominik",
"email": "[email protected]"
},
{
"id": "github|43643518",
"name": "Estibaliz Gómez-de-Mariscal",
"affiliation": "Instituto Gulbenkian de Ciência",
"orcid": "0000-0003-2082-3277",
"github_user": "esgomezm",
"email": "[email protected]"
},
{
"id": "github|75674828",
"name": "Caterina Fuster-Barceló",
"affiliation": "Universidad Carlos III de Madrid",
"orcid": "0000-0002-4784-6957",
"github_user": "cfusterbarcelo",
"email": "[email protected]"
},
{
"id": "github|17722010",
"name": "Qin Yu",
"affiliation": "European Molecular Biology Laboratory",
"orcid": "0000-0002-4652-0795",
"github_user": "qin-yu",
"email": "[email protected]"
},
{
"id": "github|32124316",
"name": "Vera Galinova",
"affiliation": "Fondazione Human Technopole",
"orcid": "0009-0001-0166-0399",
"github_user": "veegalinova",
"email": "[email protected]"
},
{
"id": "github|1878378",
"name": "Mehdi Seifi",
"affiliation": "Fondazione Human Technopole",
"orcid": "0009-0008-9276-5225",
"github_user": "mese79",
"email": "[email protected]"
},
{
"id": "github|47150974",
"name": "Iván Hidalgo-Cenalmor",
"affiliation": "Instituto Gulbenkian de Ciência",
"orcid": "0009-0000-8923-568X",
"github_user": "IvanHCenalmor",
"email": "[email protected]"
}
],
"collection_template": {
"name": "bioimage.io",
"type": "collection",
"description": "bioimage.io collection RDF",
"license": "CC0-1.0",
"tags": [],
"version": "0.3.0",
"authors": [
{
"name": "BioImgae.IO Team"
}
],
"documentation": "https://raw.githubusercontent.com/bioimage-io/collection/main/collection_json.md",
"git_repo": "https://github.com/bioimage-io/collection",
"icon": "https://raw.githubusercontent.com/bioimage-io/bioimage.io/main/public/static/icons/android-chrome-384x384.png",
"cite": [
{
"text": "todo cite BioImageIO",
"url": "https://bioimage.io"
}
],
"format_version": "0.3.0",
"config": {
"splash_title": "BioImage Model Zoo",
"splash_subtitle": "Advanced AI models in one-click",
"splash_feature_list": [
"Integrate with Fiji, Ilastik, ImJoy",
"Try model instantly with BioEngine",
"Contribute your models via Zenodo",
"Link models to datasets and applications"
],
"explore_button_text": "Start Exploring",
"background_image": "static/img/zoo-background.svg",
"resource_types": [
"model",
"application",
"dataset"
],
"default_type": "model",
"partners": [
{
"background_image": "static/img/zoo-background.svg",
"default_type": "model",
"explore_button_text": "Start Exploring",
"icon": "https://raw.githubusercontent.com/bioimage-io/bioimage.io/main/public/static/img/bioimage-io-icon.svg",
"id": "bioimageio",
"logo": "https://raw.githubusercontent.com/bioimage-io/bioimage.io/main/public/static/img/bioimage-io-icon.svg",
"name": "BioImage.IO",
"resource_types": [
"model",
"application",
"notebook",
"dataset"
],
"splash_feature_list": [
"Integrate with Fiji, Ilastik, ImJoy",
"Try model instantly with BioEngine",
"Contribute your models via Zenodo",
"Link models to datasets and applications"
],
"splash_subtitle": "Advanced AI models in one-click",
"splash_title": "BioImage Model Zoo",
"tags": []
},
{
"background_image": "static/img/zoo-background.svg",
"default_type": "application",
"explore_button_text": "Start Exploring",
"icon": "https://raw.githubusercontent.com/HenriquesLab/ZeroCostDL4Mic/master/Wiki_files/ZeroCostLogo.png",
"id": "zero",
"logo": "https://raw.githubusercontent.com/HenriquesLab/ZeroCostDL4Mic/master/Wiki_files/ZeroCostLogo.png",
"name": "ZeroCostDL4Mic",
"resource_types": [
"model",
"application",
"dataset"
],
"splash_feature_list": [],
"splash_subtitle": "A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy",
"splash_title": "ZeroCostDL4Mic",
"tags": [
"ZeroCostDL4Mic"
]
},
{
"background_image": "static/img/zoo-background.svg",
"contact": [
{
"affiliation": [
{
"name": "UC3M",
"url": "https://www.uc3m.es/home"
}
],
"email": "[email protected]",
"github": "arratemunoz",
"name": "Arrate Mu\u00f1oz Barrutia"
},
{
"affiliation": [
{
"name": "EPFL",
"url": "https://www.epfl.ch/en/"
}
],
"email": "[email protected]",
"github": "dasv74",
"name": "Daniel Sage"
}
],
"default_type": "model",
"docs": "https://github.com/deepimagej/deepimagej-plugin/wiki",
"explore_button_text": "Start Exploring",
"icon": "https://raw.githubusercontent.com/deepimagej/models/master/logos/icon.png",
"id": "deepimagej",
"logo": "https://raw.githubusercontent.com/deepimagej/models/master/logos/logo.png",
"name": "DeepImageJ",
"resource_types": [
"model",
"notebook",
"application"
],
"splash_feature_list": [],
"splash_subtitle": "A user-friendly plugin to run deep learning models in ImageJ",
"splash_title": "deepImageJ",
"tags": [
"deepimagej"
]
},
{
"background_image": "static/img/zoo-background.svg",
"contact": [
{
"affiliation": [
{
"name": "HT",
"url": "https://humantechnopole.it/en/"
}
],
"email": "[email protected]",
"github": "fjug",
"name": "Florian Jug"
}
],
"default_type": "model",
"docs": "https://imagej.net/software/fiji/",
"explore_button_text": "Start Exploring",
"icon": "https://fiji.sc/site/logo.png",
"id": "fiji",
"logo": "https://fiji.sc/site/logo.png",
"name": "Fiji",
"resource_types": [
"model",
"notebook"
],
"splash_feature_list": [],
"splash_subtitle": "Fiji is just ImageJ",
"splash_title": "Fiji",
"tags": [
"fiji"
]
},
{
"background_image": "static/img/zoo-background.svg",
"contact": [
{
"affiliation": [
{
"name": "KTH",
"url": "https://www.kth.se/en"
}
],
"email": "[email protected]",
"github": "oeway",
"name": "Wei Ouyang"
}
],
"default_type": "application",
"docs": "https://imjoy.io/docs/#/",
"explore_button_text": "Start Exploring",
"icon": "https://imjoy.io/static/img/imjoy-icon.svg",
"id": "imjoy",
"logo": "https://imjoy.io/static/img/imjoy-icon.svg",
"name": "ImJoy",
"resource_types": [
"notebook",
"application"
],
"splash_feature_list": [
"Minimal and flexible plugin powered web application",
"Server-less progressive web application with offline support",
"Rich and interactive user interface powered by web technologies"
],
"splash_subtitle": "Deep Learning Made Easy!",
"splash_title": "ImJoy",
"tags": [
"imjoy"
]
},
{
"background_image": "static/img/zoo-background.svg",
"default_type": "model",
"explore_button_text": "Start Exploring",
"icon": "https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/image/ilastik-fist-icon.png",
"id": "ilastik",
"logo": "https://raw.githubusercontent.com/ilastik/bioimage-io-resources/main/image/ilastik-fist-icon.png",
"name": "ilastik",
"resource_types": [
"model",
"application"
],
"splash_feature_list": [],
"splash_subtitle": "the interactive learning and segmentation toolkit",
"splash_title": "ilastik",
"tags": [
"ilastik"
]
},
{
"about_url": "https://www.proteinatlas.org/",
"background_image": "static/img/zoo-background.svg",
"contact": [
{
"affiliation": [
{
"name": "KTH",
"url": "https://kth.se"
},
{
"name": "Stanford",
"url": "https://stanford.edu"
}
],
"email": "[email protected]",
"github": "OmFrederic",
"name": "Frederic Ballllosera Navarro"
}
],
"default_type": "model",
"docs": "https://www.proteinatlas.org/about",
"explore_button_text": "Start Exploring",
"icon": "https://raw.githubusercontent.com/bioimage-io/tfjs-bioimage-io/master/apps/hpa-logo.gif",
"id": "hpa",
"logo": "https://raw.githubusercontent.com/bioimage-io/tfjs-bioimage-io/master/apps/hpa-logo.gif",
"name": "HPA",
"resource_types": [
"model",
"application"
],
"splash_feature_list": [],
"splash_subtitle": null,
"splash_title": "The Human Protein Atlas",
"tags": [
"hpa"
]
},
{
"background_image": "static/img/zoo-background.svg",
"default_type": "model",
"explore_button_text": "Start Exploring",
"icon": "https://raw.githubusercontent.com/Icy-imaging/icy-bioimage-io/main/icy_logo.svg",
"id": "icy",
"logo": "https://raw.githubusercontent.com/Icy-imaging/icy-bioimage-io/main/icy_logo.svg",
"name": "Icy",
"resource_types": [
"application",
"model"
],
"splash_feature_list": [],
"splash_subtitle": "Icy is an open community platform for bioimage informatics",
"splash_title": "Icy",
"tags": [
"icy"
]
},
{
"background_image": "static/img/zoo-background.svg",
"default_type": "model",
"explore_button_text": "Start Exploring",
"icon": "https://raw.githubusercontent.com/qupath/qupath-bioimage-io/main/logos/QuPath_256.png",
"id": "qupath",
"logo": "https://raw.githubusercontent.com/qupath/qupath-bioimage-io/main/logos/QuPath_256.png",
"name": "QuPath",
"resource_types": [
"application",
"model"
],
"splash_feature_list": [],
"splash_subtitle": "QuPath is open-source software for bioimage analysis and digital pathology",
"splash_title": "QuPath",
"tags": [
"qupath"
]
},
{
"background_image": "static/img/zoo-background.svg",
"contact": [
{
"email": "[email protected]",
"github": "uschmidt83",
"name": "Uwe Schmidt"
},
{
"affiliation": [
{
"name": "EPFL",
"url": "https://www.epfl.ch/en/"
}
],
"email": "[email protected]",
"github": "maweigert",
"name": "Martin Weigert"
}
],
"default_type": "model",
"docs": "https://github.com/stardist/stardist",
"explore_button_text": "Start Exploring",
"icon": "https://raw.githubusercontent.com/stardist/stardist-bioimage-io/main/logos/stardist_256.png",
"id": "stardist",
"logo": "https://raw.githubusercontent.com/stardist/stardist-bioimage-io/main/logos/stardist_256.png",
"name": "StarDist",
"resource_types": [
"application",
"model"
],
"splash_feature_list": [],
"splash_subtitle": "StarDist - object detection with star-convex shapes",
"splash_title": "StarDist",
"tags": [
"stardist"
]
},
{
"background_image": "static/img/zoo-background.svg",
"contact": [
{
"affiliation": [
{
"name": "DIPC",
"url": "https://dipc.ehu.eus/en"
}
],
"email": "[email protected]",
"github": "danifranco",
"name": "Daniel Franco-Barranco"
}
],
"default_type": "model",
"docs": "https://biapy.readthedocs.io/en/latest/",
"explore_button_text": "Start Exploring",
"icon": "https://raw.githubusercontent.com/BiaPyX/BiaPy-bioimage-io/main/logos/BiaPy_256.png",
"id": "biapy",
"logo": "https://raw.githubusercontent.com/BiaPyX/BiaPy-bioimage-io/main/logos/BiaPy_256.png",
"name": "BiaPy",
"resource_types": [
"model",
"application"
],
"splash_feature_list": [],
"splash_subtitle": "BiaPy is an open source Python library for building bioimage analysis pipelines",
"splash_title": "BiaPy",
"tags": [
"BiaPy"
]
},
{
"background_image": "static/img/zoo-background.svg",
"default_type": "application",
"explore_button_text": "Start Exploring",
"icon": "https://raw.githubusercontent.com/HenriquesLab/DL4MicEverywhere-bioimage-io/main/logo/dl4miceverywhere-logo-small.png",
"id": "dl4miceverywhere",
"logo": "https://raw.githubusercontent.com/HenriquesLab/DL4MicEverywhere-bioimage-io/main/logo/dl4miceverywhere-logo-small.png",
"name": "DL4MicEverywhere",
"resource_types": [
"application",
"model"
],
"splash_feature_list": [],
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]
},
{
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{
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{
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"url": "https://www.helmholtz-munich.de/en/ife/research-groups/schmoller-lab"
}
],
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"name": "Francesco Padovani"
}
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"explore_button_text": "Start Exploring",
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"bird": "🐦",
"blowfish": "🐡",
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"cat": "🐈",
"chick": "🐤",
"chicken": "🐔",
"chipmunk": "🐿",
"cow": "🐄",
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"crocodile": "🐊",
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"dolphin": "🐬",
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"gorilla": "🦍",
"hamster": "🐹",
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"hippo": "🦛",
"honeybee": "🐝",
"horse": "🐎",
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"potato": "🥔",
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"rice": "🍚",
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]
},
"notebook": {
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"briefs": "🩲",
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