bio-imaging-mass-cytometry-data-preprocessing
Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization. Use when starting IMC analysis from raw MCD files or preparing images for segmentation.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-imaging-mass-cytometry-data-preprocessing --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: anndata 0.10+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scipy 1.12+, steinbock 0.16+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # IMC Data Preprocessing **"Preprocess my imaging mass cytometry data"** → Load MCD files, apply hot pixel removal, channel cropping, and signal normalization to prepare multiplexed images for segmentation and analysis. - CLI: `steinbock preprocess` for automated IMC preprocessing pipeline ## Load MCD Files with steinbock ```bash # steinbock CLI workflow (Docker-based) # Convert MCD to TIFF steinbock preprocess imc \ --mcd raw/*.mcd \ --panel panel.csv \ -o img # Output: img/*.tiff (one per acquisition) ``` ## Panel File Format ```csv # panel.csv channel,name,keep,ilastik 1,DNA1,1,1 2,CD45,1,1 3,CD3,1,0 4,CD8,1,0 5,CD4,1,0 ``` ## Python-Based Loading ```python import
- Version Compatibility
- Load MCD Files with steinbock
- Panel File Format
- Python-Based Loading
- Hot Pixel Removal
- Spillover Correction
- Estimate Spillover from Single-Stain Controls
- Image Normalization
- steinbock Preprocessing Pipeline
- Visualize with napari
- Create AnnData Object
- Batch Processing
- Related Skills
steinbock CLI workflow (Docker-based) Convert MCD to TIFF steinbock preprocess imc \ Complete preprocessing with steinbock steinbock preprocess imc --mcd raw/*.mcd -o img steinbock preprocess filter --img img -o img_filtered Requires trained Ilastik classifier steinbock classify ilastik \
What does the bio-imaging-mass-cytometry-data-preprocessing skill do?
Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization. Use when starting IMC analysis from raw MCD files or preparing images for segmentation.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-imaging-mass-cytometry-data-preprocessing --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.