Software

Multi-layer region-of-interest annotation for whole-slide microscopy, hyperspectral cubes, and rasters — exports binary, labelled, and multi-class masks (GeoJSON, QuPath, TIFF) with a resumable Shiny/OpenSeadragon batch annotator.

Statistical analysis and audit-ready reporting pipeline for routine cell-culture diagnostics with microscopic evaluation.

Reading, QC, phenotyping, spatial statistics, and visualisation of single-cell spatial biology data from multiplexed imaging platforms.

End-to-end R pipeline for longitudinal MRI and CT analysis in spinal-cord injury research (wraps Spinal Cord Toolbox, dcm2niix, pydicom).

Cell segmentation for histology and multiplexed tissue imaging with human-in-the-loop training — classical methods plus Cellpose, StarDist, and Mesmer.

Experimental package for calibrated histology burden measurements, traceable review, reporting and Shiny exploration of saved results; native whole-slide inference and portable DNN training are not yet qualified end to end.

1.0.0 release candidate defining the cellspec table contract for segmented cells: import, validation, signal policies and integrity-checked exchange. External fixture comparisons and CRAN submission remain pending.

1.0.0 release candidate for marker callability, thresholds, phenotype classification and Shiny review, with immutable snapshots and verifiable exports; preparation for first CRAN submission is ongoing.

R bindings to the Cubert CUVIS SDK for reading, calibrating, and exporting hyperspectral camera data.

Publication-grade artistic visualisation of hyperspectral imagery, built on the hyperspectR cube class.

Complete R pipeline for biomedical hyperspectral imaging — from raw camera data to clinical tissue oxygenation maps.

Vendor-agnostic analysis and visualisation of Laser-Induced Breakdown Spectroscopy (LIBS) data, with a focus on biomedical tissue applications.

Pure-R reader for Diaspective Vision TIVITA hyperspectral recordings — parses the SpecCube container, acquisition metadata and exported parameter images, with no vendor SDK required.

Streamlined RNA-seq analysis pipelines — from count matrices to publication-ready results.

Unified R platform for molecular pathology data — parses NGS files (VCF, BAM, FASTQ), XML/PDF reports, and clinical data into a queryable database with an interactive Shiny app.

Auditor live-evaluation dashboard for haematological oncology cohorts — quality and coverage indicators, OPS-coded complex-therapy and diagnostics counts, Kaplan–Meier, oncoprint, and cytogenetics summaries in an interactive Shiny app.

Unofficial R client for the SeaTable REST API — read, write, and sync collaborative cloud databases from R.

Parser for NONMEM .lst output files — extracts THETA / OMEGA / SIGMA estimates into tidy data frames for population PK/PD analysis.

Parsing, analysis, and visualisation of capacitive pressure-distribution data — insoles, saddles (equine and bicycle), seating, and barefoot pedography.

Pure-R parser for the binary .Q-View project file format used in chemiluminescent multiplex ELISA plate imaging and quantification.

Domain-neutral analysis and visualisation layer for discrete-event, agent-based, and node-actor simulation outputs.

Reproducible, question-driven, embedding-aware science mapping — a toolkit for bibliometric and scientometric analysis.

Native R/C++ implementation of SONG (Self-Organizing Nebulous Growths) for nonlinear dimensionality reduction and visualisation.

Generate polished hex sticker logos for R packages using customizable templates.

Custom workflowr themes and templates for reproducible research websites in R.

Shared pkgdown template giving the CTTIR package suite a unified look — Hugo Coder palette with a light/dark toggle.

Merges duplicate Zotero items by DOI only — keeps the newest record's fields, unions collections, tags, and attachments inside one transaction.

Detects and resolves duplicate file attachments by content hash — auto-removes byte-identical bare copies, prompts a review dialog for annotated PDFs.

Reconciles and completes item metadata against PubMed, OpenAlex, Crossref, Semantic Scholar, OpenAIRE, Unpaywall, CORE, and CRAN.

Offline-first Progressive Web App for collecting questionnaire responses in research and field settings — exports sessions as QR codes or CSV / XLSX / TXT / XML.

Desktop launchpad for package apps, staged Shiny source apps and hosted HTTPS URLs. Version 0.1.0 has a GitHub release; 0.2.0-rc.1 is an unpublished release candidate with platform qualification still pending.

Development R/Shiny application for classroom brainwriting, with timed rounds, QR-code participation, SQLite persistence, mobile reconnect support and German, English and French interfaces.

Repository placeholder: currently empty, with no published implementation or installation instructions.