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data-preprocessing

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Load and preprocess imaging mass cytometry (IMC) and MIBI data from raw MCD/TXT through hot-pixel removal, spillover compensation, and variance-stabilizing transformation, covering readimc/steinbock ingestion, NNLS spillover compensation (CATALYST), IMC-Denoise, and the IMC arcsinh-cofactor question. Use when starting analysis from raw MCD files, building per-channel TIFF stacks, compensating channel spillover, choosing an arcsinh cofactor, or preparing single-cell intensities for phenotyping.

When to use

• starting analysis from raw MCD files
• building per-channel TIFF stacks
• compensating channel spillover
• choosing an arcsinh cofactor
• preparing single-cell intensities for phenotyping
• hot-pixel removal
• variance-stabilizing transformation
• ingesting IMC and MIBI data

When not to use

• using 3x3 median filter for denoising
• using flow-style spillover compensation (exact matrix inverse)
• using arcsinh cofactor 5 for IMC single-cell means
• quantifying per-pixel expression
• compensating channels driven above ~5,000 dual counts

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