Package: cellspecR 1.1.0

R. Heller

cellspecR: Read, Validate and Store Multiplexed Imaging Cell Tables

Defines 'cellspec', a versioned table format for segmented cells from multiplexed tissue images: cell identifiers, centroids in micrometres, per-marker measurements with an explicit compartment and statistic, image and channel metadata, and provenance. Reads measurement exports of image-analysis tools such as 'QuPath' and 'MCMICRO' into this format, validates its structure and content, selects one signal per marker through an explicit policy, and writes directories with a 'SHA-256' checksum manifest so that later analysis steps can verify what they read. 'QuPath' is described by Bankhead et al. (2017) <doi:10.1038/s41598-017-17204-5> and 'MCMICRO' by Schapiro et al. (2022) <doi:10.1038/s41592-021-01308-y>.

Authors:R. Heller [aut, cre, cph]

cellspecR_1.1.0.tar.gz
cellspecR_1.1.0.zip(r-4.7-any)cellspecR_1.1.0.zip(r-4.6-any)cellspecR_1.1.0.zip(r-4.5-any)
cellspecR_1.1.0.tgz(r-4.6-any)cellspecR_1.1.0.tgz(r-4.5-any)
cellspecR_1.1.0.tar.gz(r-4.7-any)cellspecR_1.1.0.tar.gz(r-4.6-any)
cellspecR_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cellspecR/json (API)

# Install 'cellspecR' in R:
install.packages('cellspecR', repos = c('https://cttir.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cttir/cellspecr/issues

Pkgdown/docs site:https://cttir.github.io

On CRAN:

Conda:

4.18 score 39 exports 6 dependencies

Last updated from:bd940f1baf. Checks:8 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK180
source / vignettesOK401
linux-releaseOK166
macos-releaseFAIL60
macos-oldrelOK142
windows-develOK128
windows-releaseOK136
windows-oldrelOK105
wasm-releaseOK112

Exports:cs_adjacencycs_appcs_as_anndatacs_as_specs_assert_validcs_bindcs_cellscs_channelscs_column_mapcs_detect_formatcs_dictionarycs_examplecs_feature_supportcs_featurescs_formatscs_from_specs_imagescs_marker_mapcs_markerscs_measurementscs_merge_tilescs_newcs_provenancecs_readcs_read_cellspeccs_read_npycs_read_npzcs_read_signal_policycs_signal_matrixcs_signal_policycs_spec_versioncs_validatecs_verifycs_vocabularycs_writecs_write_npycs_write_npzcs_write_signal_policyis_cellspec

Dependencies:clidata.tabledigestjsonlitenanoparquetrlang

Adapter reference
Rendered fromadapters-reference.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-09-15

Getting started with cellspecR
Rendered fromcellspecR.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-09-15

Interoperability with SpatialExperiment and AnnData
Rendered frominteroperability.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-09-15

Reading cell measurement exports
Rendered fromreading-exports.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-09-15

The cellspec 1.0 format
1. Object | 2. Cells | 3. Measurements | 4. Dictionary | 5. Images and channels | 6. Provenance | 7. Adjacency (optional) | 8. Coordinate frame and units | 9. Directory layout | 10. Validation rules | 11. Versioning
Rendered fromspecification.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-09-15

Readme and manuals

Help Manual

Help pageTopics
Subset a cellspec object by cells and features[.cellspec
Convert a cellspec object to a data frameas.data.frame.cellspec as_tibble.cellspec
Print, summarise and measure a cellspec objectcellspec-methods dim.cellspec print.cellspec print.cellspec_summary summary.cellspec
Access the components of a cellspec objectcs_accessors cs_adjacency cs_cells cs_channels cs_dictionary cs_images cs_measurements cs_provenance
Create the cellspec review applicationcs_app
Convert a cellspec object to AnnDatacs_as_anndata
Convert a cellspec object to SpatialExperimentcs_as_spe
Combine cellspec objects from different imagescs_bind
Validate a table column mapcs_column_map
Detect the generic table formatcs_detect_format
A small synthetic cellspec objectcs_example
Summarise the signal support of features per imagecs_feature_support
Select features and markers by their dictionary entriescs_features cs_markers
List the available cellspec readerscs_formats
Convert a SpatialExperiment back to cellspeccs_from_spe
Create a marker-name mappingcs_marker_map
Merge tiled cellspec objects using centroid ownershipcs_merge_tiles
Create a cellspec objectcs_new
Read a delimited table into a cellspec objectcs_read
Read a canonical cellspec directorycs_read_cellspec
Read and write NumPy array filescs_read_npy cs_read_npz cs_write_npy cs_write_npz
Read a signal policy from JSON or CSVcs_read_signal_policy
Select one signal per cell and markercs_signal_matrix
Create a signal selection policycs_signal_policy
Version of the cellspec specificationcs_spec_version
Validate a cellspec objectcs_assert_valid cs_validate
Verify a canonical cellspec directorycs_verify
Columns and controlled vocabularies of the cellspec formatcs_vocabulary
Write a cellspec directorycs_write
Write a signal policy as JSON or CSVcs_write_signal_policy
Test for a cellspec objectis_cellspec
Plot cellspec quality-control viewsplot.cellspec