Package: scivision
If you are new to Scivision, start with thewebsite.The Scivision project is building:Some things hosted inthis GitHub repository:Acatalogof community-curated computer visionmodelsanddatasetsfrom the sciences and humanitiesAPython package, for conveniently downloading and using these models and datasets from Python (scivision on PyPI)Documentationfor the above (documentation website)Agallery of notebooksusing Scivision models and datasetsacommunityof computer vision practitioners in the sciences and humanities
(mailing list,get Slack invitation)A (nascent)ecosystem of computer vision tools and utilitiesSubmit a bug or feature requesthere.If you would like a link to a model or datasource to be listed in the catalog, such a contribution would be gratefully received. See theContributing Guidefor how to set up and submit a new entry.  Pull requests for code changes are also welcome.The Scivision project is funded by the Alan Turing Institute.Repository contentsThe mainproject repository on GitHubhostsdevelopment of the Python package (in the root directory)development of the website (infrontend)the documentation sources (indocs)Getting StartedA quick overview of using the Scivision.Py python package.Install Scivision.Py$pipinstallscivisionFull installation guideLoad a Scivision modelfromscivisionimportload_pretrained_modelresnet18=load_pretrained_model(# The model URL"https://github.com/alan-turing-institute/scivision_classifier",# A Scivision model can contain several variants -- below we select the one to usemodel_selection='resnet18',# Allow the model and its dependencies to be installed if they are not already# (including tensorflow in this example)allow_install=True)We can give an image as input to the model.  Any image data compatible with numpy (an 'Array_like') is accepted.
We can obtain some image data by loading a Scivision datasource.More about Scivision modelsLoad a Scivision datasourcefromscivisionimportload_pretrained_modeldataset=load_dataset('https://github.com/alan-turing-institute/scivision-test-data')# 'dataset' provides several named arrays.  This datasource provides one named 'test_image':# the keys can be looked up with `list(dataset)` (or by consulting the datasource documentation)#test_image=dataset['test_image'].read()Optionally, inspect the image (with matplotlib, for example):importmatplotlib.pyplotaspltplt.imshow(test_image)More about datasourcesRun a Scivision modelresnet.predict(test_image)Output:koala : 99.78%Query the model and datasource catalogsfromscivisionimportdefault_catalog# The datasource catalog as a Pandas dataframedefault_catalog.data.to_dataframe()# Similarly for the model catalogdefault_catalog.models.to_dataframe()Output:namedescriptiontasksurlpkg_urlformatscivision_usablepretrainedlabels_requiredinstitutiontags0stardistSingle class object detection and segementation of star-convex polygons(<TaskEnum.object_detection: 'object-detection'>, <TaskEnum.segmentation: 'segmentation'>)https://github.com/stardist/stardistgit+https://github.com/stardist/stardist.git@masterimageFalseTrueTrue('epfl',)('2D', '3D', 'optical-microscopy', 'xray', 'microtomography', 'cell-counting', 'plant-phenotyping', 'climate-change-and-agriculture')1PlantCVOpen-source image analysis software package targeted for plant phenotyping(<TaskEnum.segmentation: 'segmentation'>, <TaskEnum.thresholding: 'thresholding'>, <TaskEnum.object_detection: 'object-detection'>)https://github.com/danforthcenter/plantcvgit+https://github.com/danforthcenter/plantcv@mainimageFalseTrueTrue('danforthcenter',)('2D', 'hyperspectral', 'multispectral', 'near-infrared', 'infrared', 'plant-phenotyping', 'climate-change-and-agriculture')⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮⋮Contributing an entry to the catalogThe catalogs are browsable online:model catalogdatasource catalogContributorsThanks goes to these wonderful people (emoji key):Aida Mehonic📋📖🤔Alan R Lowe💻🤔📖🚇🔍Alejandro ©💻🤔🎨💡Beatriz Costa Gomes💻🤔📖🎨💡Ben Evans🤔Ed Chalstrey💻🤔📖🚇Eriol Fox🤔🎨Evangeline Corcoran💻🤔📖🚇Isabel Fenton💻🤔📖🚇James Parkhurst🤔🔣🔌JamesAliScott🤔🔣Kasra Hosseini💻🤔📖🚇Martin Rogers🔣💡💻🤔Miquel Massot💻🤔📖🔌Robert Blackwell🤔Samuel Tonks💻🤔📖🚇Scott Hosking🔍🤔Seb Hickman💡📢nbarlowATI🤔📋💡ots22💻🤔📖🚇pwochner🤔📋💡vimode🤔🎨💻️️️️♿️This project follows theall-contributorsspecification. Contributions of any kind welcome!