cellspecR: Read, Validate and Store Multiplexed Imaging Cell Tables

cellspecR defines cellspec, one table format for segmented cells from multiplexed tissue images, reads the exports of common image-analysis tools into it, checks the result, and writes it to disk with a checksum manifest so that later analysis steps can prove what they read.

The format is described in vignette("specification", package = "cellspecR").

Main functions

• Specification: cs_spec_version(), cs_vocabulary().

• Object: cs_new(), cs_cells(), cs_measurements(), cs_dictionary(), cs_images(), cs_channels(), cs_provenance(), cs_adjacency(), cs_features(), cs_markers(), is_cellspec().

• Methods: print.cellspec(), summary.cellspec(), dim.cellspec(), [.cellspec, as.data.frame.cellspec().

See also

Useful links:

• https://github.com/CTTIR/cellspecR

• https://cttir.github.io/cellspecR/

• Report bugs at https://github.com/CTTIR/cellspecR/issues

Author

Maintainer: R. Heller raban.heller@uni-ulm.de (ORCID) [copyright holder]

Authors:

• R. Heller raban.heller@uni-ulm.de (ORCID) [copyright holder]