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bio-imaging-mass-cytometry-interactive-annotation

Maintainer FreedomIntelligence · Last updated April 1, 2026

Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation validation. Use when manually annotating cell types for training classifiers or validating automated phenotyping results.

OpenClawNanoClawTrainingEvaluationbio-imaging-mass-cytometry-interactive-annotation🧬 bioinformatics (gptomics bio-* suite)bioinformatics — immunoinformatics & flow cytometryinteractive

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-imaging-mass-cytometry-interactive-annotation

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Python: napari.Viewer() with label layer for interactive annotation.
  • Manually annotate cell types in my IMC data" → Interactively label cells using napari visualization with marker overlays for training classifiers or validating automated phenotyping results. Python: napari.Viewer() with label layer for interactive annotation.
  • image_stack = io.imread('imc_image.tiff') # (C, H, W) segmentation_mask = io.imread('cell_segmentation.tiff').

Source Doc

Excerpt From SKILL.md

Napari-Based Annotation

import napari
import numpy as np
from skimage import io
import pandas as pd

## Add channels as separate layers for visualization

channel_names = ['CD45', 'CD3', 'CD68', 'panCK', 'DNA']
for i, name in enumerate(channel_names):
    viewer.add_image(image_stack[i], name=name, visible=False, colormap='gray', blending='additive')

## Add segmentation

viewer.add_labels(segmentation_mask, name='Cells')

Use cases

  • Use when manually annotating cell types for training classifiers or validating automated phenotyping results.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • cell-segmentation - Generate cell masks for annotation
  • phenotyping - Automated phenotyping as alternative
  • spatial-analysis - Use annotations for spatial analysis
  • quality-metrics - QC annotated data

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