Package {grayleafspotdata}

Type: Package
Title: File Manifest for the S-BSST3199 Magnaporthe Colony Image Dataset
Version: 0.1.0
Date: 2026-08-19
Description: Provides a machine-readable file and image manifest for the research data deposited in EMBL-EBI BioStudies under accession S-BSST3199 (a time-series petri-dish image dataset of Magnaporthe colonies from twelve plates, with associated morphometric analysis outputs produced by metrics-petri 3.0.0). The original research files are not bundled in this R package; they remain hosted by BioStudies. The manifest can be used in image-analysis and plant-pathology workflows, including workflows based on the 'grayleafspotr' software. Related research outputs are documented using their persistent identifiers.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Maintainer: Rohan R <phonics-tiffs1i@icloud.com>
URL: https://github.com/rotsl/grayleafspotdata, https://www.ebi.ac.uk/biostudies/studies/S-BSST3199, https://rotsl.r-universe.dev/
BugReports: https://github.com/rotsl/grayleafspotdata/issues
Depends: R (≥ 3.5.0)
Suggests: testthat (≥ 3.0.0)
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-08-20 03:10:26 UTC; tslwork
Author: Rohan R ORCID iD [aut, cre]
Repository: CRAN
Date/Publication: 2026-08-21 15:30:09 UTC

Top-level deposited file manifest for S-BSST3199

Description

A machine-readable manifest of the six top-level research files deposited directly in the BioStudies record S-BSST3199 (excluding the macOS .DS_Store artifact). These are the files listed in the deposited SHA256SUMS.txt checksum file. SHA-256 values and file sizes are populated because BioStudies exposes them at this level.

Use this dataset to verify the integrity of the deposited archive without downloading every byte of raw_images.zip, or to locate each top-level file's canonical BioStudies URL.

Format

A data frame with 6 rows and one row per deposited top-level file. Columns:

file_id

Integer row identifier, 1 to 6.

filename

Flattened filename as served by the BioStudies file URL endpoint (e.g. README.txt, metrics-petri-3.0.0.zip).

relative_path

Path inside the BioStudies deposit as recorded in SHA256SUMS.txt (e.g. metadata/dataset_manifest.csv, software/metrics-petri-3.0.0.zip).

extension

File extension, lowercased.

media_type

Declared media type.

file_size_bytes

File size in bytes, from the BioStudies files API.

sha256

SHA-256 checksum from the deposited SHA256SUMS.txt, lowercase hexadecimal.

study_accession

BioStudies accession, S-BSST3199.

study_url

Canonical BioStudies study URL.

biostudies_file_url

Direct BioStudies file URL.

description

Description of the file as listed by the BioStudies files API.

Source

EMBL-EBI BioStudies accession S-BSST3199. Files API listing retrieved 2026-08-18 from https://www.ebi.ac.uk/biostudies/api/v1/studies/S-BSST3199/files. SHA-256 values retrieved 2026-08-18 from https://www.ebi.ac.uk/biostudies/files/S-BSST3199/SHA256SUMS.txt.

References

EMBL-EBI BioStudies accession S-BSST3199, DOI doi:10.6019/S-BSST3199.

Image manifest for the S-BSST3199 Magnaporthe colony dataset

Description

A machine-readable manifest describing the 49 source image files associated with the research dataset deposited in EMBL-EBI BioStudies under accession S-BSST3199. The study is titled "Time-series Magnaporthe colony images from twelve petri dishes and morphometric analysis results generated using metrics-petri 3.0.0".

The original image files are not bundled with this R package. They remain available from the authoritative BioStudies record at https://www.ebi.ac.uk/biostudies/studies/S-BSST3199.

This manifest can be used on its own, or together with image-analysis software such as grayleafspotr. No R-level dependency on grayleafspotr is introduced.

Format

A data frame with 49 rows and one row per deposited source image. Columns:

file_id

Integer row identifier, 1 to 49.

filename

Original image filename as listed in dataset_manifest.csv (e.g. 20260204_P001_30JAN_WT_PCBM_CTRL_d05_TOP.JPG).

relative_path

Inferred path of the image inside the BioStudies deposit (e.g. raw_images/30jan/20260204_P001_30JAN_WT_PCBM_CTRL_d05_TOP.JPG). Derived from the directory pattern of the related metadata_file value. Never an absolute path.

extension

File extension, lowercased (e.g. .jpg).

media_type

Declared media type (e.g. image/jpeg).

file_size_bytes

File size in bytes. NA when not available from the deposited metadata. The 49 individual images are packaged inside raw_images.zip; per-image sizes are not exposed separately by the BioStudies record.

sha256

SHA-256 checksum as lowercase hexadecimal. NA for individual image rows because the BioStudies SHA256SUMS.txt only publishes top-level deposit checksums. Populate this column by re-running data-raw/build_manifest.R against a local copy of the dataset directory.

study_accession

BioStudies accession, S-BSST3199.

study_repository

Hosting repository name, EMBL-EBI BioStudies.

study_url

Canonical BioStudies study URL.

biostudies_file_url

Direct BioStudies file URL when one can be established. NA for individual image rows because the images are inside raw_images.zip, not directly retrievable per-image.

acquisition_group

Acquisition group identifier as listed in dataset_manifest.csv: 30jan or 6feb.

plate_id

Plate identifier as listed in dataset_manifest.csv: P001 for the 30 January group, P02 to P12 for the 6 February group.

metadata_file

Path of the plate-level image_metadata.csv file as listed in dataset_manifest.csv.

analysis_directory

Path of the plate-level analysis output directory as listed in dataset_manifest.csv.

organism

Study-level organism. The BioStudies record identifies the colonies as Magnaporthe; propagated to all rows.

metadata_source

Free-text provenance note describing where the per-row values were obtained from.

local_manifest_source

Identifier of the local source directory used by data-raw/build_manifest.R when per-image checksums were computed. NA in the published build because the build was generated from the remote BioStudies record only.

Source

EMBL-EBI BioStudies accession S-BSST3199, file dataset_manifest.csv. Retrieved 2026-08-18 from https://www.ebi.ac.uk/biostudies/files/S-BSST3199/dataset_manifest.csv. Study landing page: https://www.ebi.ac.uk/biostudies/studies/S-BSST3199.

References

Related research outputs include: