domains / families / science / interactive-annotation

interactive-annotation

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Interactive cell annotation and image QC for IMC/MIBI using napari, napari-imc, Mantis Viewer, and cytomapper, covering the pixels-to-cell-table bridge, overlaying masks to catch segmentation/spillover artifacts, inter-annotator variability as the accuracy ceiling, contrast-as-threshold, and building class-balanced ground-truth label sets. Use when manually labeling cells, generating training data for a classifier, QC-ing segmentation on the image, confirming clusters are spatially real, or choosing an annotation viewer.

When to use

• manually labeling cells
• generating training data for a classifier
• QC-ing segmentation on the image
• confirming clusters are spatially real
• choosing an annotation viewer
• overlaying masks to catch segmentation/spillover artifacts
• building class-balanced ground-truth label sets

Skill page

Source