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Changelog

Source: NEWS.md

cellspecR 1.1.0

  • Functions released in 1.0.0 are no longer marked experimental; like the package, they are stable. The NumPy readers and writers added in this version are experimental.

  • The MCQuant, segmantR and inForm readers derive image and sample identifiers of an RDS table from its file name, as for delimited files; before, they came from a temporary copy and differed between reads.

  • Standardize the named v5 package logo across README, documentation pages and available application headers, with matching light and dark artwork.

  • cs_read_npy() and cs_read_npz() read NumPy array files and archives in base R (booleans, integers, floats, complex, fixed-width strings; C or Fortran order); cs_write_npy() and cs_write_npz() write them without an external zip program.

  • Signal policies can declare separate preferred and fallback finite domains, including negative finite measurements. Existing minimum-domain defaults and five-column policies remain unchanged. Extended seven-column policies preserve both domains through JSON and CSV.

  • Signal-policy I/O preserves structured error classes when parser diagnostics or paths contain literal braces.

  • Canonical TSV decimal conversion now preserves double precision on platforms where extended precision equals double precision, including macOS ARM. The 17-digit file format and exact-value round-trip contract are unchanged.

  • Header-only TSV exports now write a complete gzip stream, including empty cell and adjacency tables. Their declared column types survive read-back.

  • QuPath readers recognize compartment-first cell area and nuclear morphology with explicit units. Whole-cell area is kept separately from nuclear area; shape dictionaries retain the original headers and dimensional units.

  • The segmantR reader converts one-based pixel-index centroid means to the image’s pixel-edge coordinate frame and converts pixel area to square micrometres. Unrecognised centroid conventions are rejected. Crop, pyramid and anisotropic transforms must be handled explicitly before image integration. Raw shape measurements retain their pixel or radian units.

  • cs_formats() reports segmantR 0.2.0, the version the segmantR reader was tested with, instead of the non-existent segmantR 0.5.

  • cs_write(overwrite = TRUE) now replaces only an empty directory or earlier cs_write() output: a directory whose cellspec.json carries the cellspec format marker and which holds no files other than those cs_write() creates. Any other directory is left untouched and an error names the unexpected entries.

  • Tiled QuPath done markers with header_sha256 now verify header lines longer than 1,024 bytes instead of reporting a missing header, and check the decompressed header line of gzip-compressed (.gz) tiles instead of their compressed bytes.

  • cs_app() now applies max_upload_mb as the Shiny upload limit while the application runs and restores the previous limit when it stops; uploads were previously capped at the 5 MB Shiny default.

  • The default plot() overview leaves out the area panel when the cells table has no area column and the marker panel when there are no intensity features, instead of failing.

  • cs_as_anndata() now defaults to policy = NULL and derives the policy the same way as cs_as_spe().

  • other features whose source names clean to the same identifier are numbered with make.unique(sep = "_") instead of aborting the read. This covers unmapped numeric columns kept by keep_other = TRUE and measurements mapped with kind = "other", also with keep_other = FALSE. Suffixes already in use are skipped: columns “a b”, “a_b” and “a_b_1” become other:a_b, other:a_b_2 and other:a_b_1.

  • summary() and its print method handle valid objects without images.

  • cs_read_cellspec() checks the row counts declared in cellspec.json before reading and reports a missing or malformed n_rows as a cellspec_error_format.

  • cs_write() no longer advances the session random number generator when it names its staging and backup directories.

  • Gzip-compressed tables and canonical tsv.gz files are decompressed in R on every platform instead of through an external gzip program. The result is checked against the gzip trailer (CRC-32 and length), so a truncated or corrupt file raises a cellspec_error_format instead of loading only part of its rows. A file whose tail was zero-filled back to its original size counts as truncated. BGZF files (bgzip) are checked block by block, may hold nothing but BGZF blocks and must end with the BGZF end-of-file block; other files made of several gzip members, which cannot be checked completely, are read with a cellspec_warning_integrity warning.

  • cellspecR now requires data.table 1.17.0 or later. Earlier versions write fwrite(compress = "gzip") output as several gzip members, which cs_read_cellspec() cannot fully check, so it would warn on the tsv.gz files written by cs_write().

cellspecR 1.0.0

First public release, on GitHub.

Specification

  • Added the cellspec 1.0 table contract, JSON Schema and vocabulary tables for segmented cells from multiplexed tissue images.

Readers

  • Added readers for QuPath, tiled QuPath, MCQuant, segmantR, inForm and mapped generic CSV/TSV tables, with format detection and provenance records.

Validation

  • Added structural and semantic validation, actionable reports, feature support summaries and deterministic synthetic examples.

Canonical format

  • Added Parquet storage with an exact text fallback, JSON sidecars, SHA-256 manifests, completion markers and atomic staging.

Signals

  • Added explicit signal policies, marker maps and selected signal matrices with JSON and CSV persistence.

Interoperability

  • Added guarded conversion to and from SpatialExperiment and AnnData objects.

Methods

  • Added tile binding and merge helpers, cellspec subsetting and coercion, and quality-control map, marker, support, area and overview plots.

Interactive front-end

  • Added a local Shiny review app for reading exports, inspecting validation and downloading review tables.