usnistgov / WIPP-backend

Web Image Processing Pipeline (WIPP) - backend
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Convert WIPP 3.0 plugin for converting WDZT annotations to masks #16

Closed pbajcsy closed 4 years ago

pbajcsy commented 5 years ago

Description (Include problem, use cases, benefits, and/or goals) Problem: Users can create image annotations using the WDZT visualization and download a JSON file per image. However, users cannot use the annotated images for AI model training unless a plugin for converting annotations to image masks is available. Use cases: AI-based segmentation for RPE cells, concrete samples, and organelle videos cannot be executed unless the manual annotations provided by experts are converted to training image masks. Benefits: users will be able to annotate and train AI-based models in WIPP 3.0 Goals: create a WIPP 3.0 plugin that takes a collection of JSON files (annotations from a collection of images) and generates a collection of image masks. The plugin will have user-specified options whether the masks should follow color, text, or shape attributes of annotations when assigning semantic labels.

Proposal (A clear and concise description of what you want to happen) Create a WIPP 3.0 plugin with the conversion code.

Additional context (Add any other context or screenshots about the feature request here) Starting point is in https://gitlab.nist.gov/gitlab/WIPP/WIPP-annotation2mask-plugin

MyleneSimon commented 4 years ago

Plugin is available here: https://github.com/usnistgov/WIPP-annotations2masks-plugin Support for annotations in WIPP in #133