CellPick#
CellPick is a computational tool for facilitating the selection of cells for laser microdissection in single cell proteomics applications. It introduces a custom shape selection technique that employs a combinatorial optimization procedure for the selection of cells, ensuring the selection of non-contiguous shapes, while approximately maximizing coverage within a restricted tissue area.
Key Features#
Flexible Data Loading: Load microscopy images (TIFF, CZI) or SpatialData (.zarr) stores with multi-channel support
Multi-resolution Support: Work with large images using adaptive resolution loading
Spatial Gradient Analysis: Establish gradients between landmarks to correlate protein intensities with cell positions
Smart Cell Selection: Multiple algorithms for selecting non-contiguous cells (k-center, random, per-region, per-label)
Label-based Selection: Load cell type labels and select cells stratified by label
Per-channel Controls: Fine-tune visibility and saturation for each channel independently
Comprehensive Export: Export to XML (LMD-compatible) or SpatialData formats
Get started with cellpick installation via pip, pipx, or conda.
Learn how to launch the cellpick application.
Step-by-step guide to the complete cellpick workflow.
Reference for all keyboard shortcuts and mouse controls.
Detailed documentation of the cellpick API.