Computational Trauma and Tissue Injury Research

Reproducible computational tools, analyses, and teaching resources for trauma and tissue injury research.

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CTTIR develops open-source software, reproducible analysis pipelines, and educational materials at the interface of trauma surgery, tissue injury, and computational biomedicine. Our work spans biomarker discovery, multi-modal imaging, dimensionality reduction, molecular pathology, and clinical-translational data science.

CTTIR R packages, grouped by theme, plus the externally maintained lstparsR companion.

Public repository coverage checked on 14 October 2026. Repository visibility does not establish a stable release, clinical validity or production readiness.

Status   ●●● published  ·  ●●○ usable  ·  ●○○ draft  ·  ○○○ idea

DOI   ⧗ previously reserved identifier; registration remains unverified.

Package	Status	DOI	Description
annotatR	●●○	⧗	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
bloodspottR	●○○	—	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.
cellreportR	●●○	⧗	Statistical analysis and audit-ready reporting pipeline for routine cell-culture diagnostics with microscopic evaluation
cellspecR	●●○	—	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.
gatekeepR	●●○	—	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.
phenoscapR	●●○	⧗	Reading, QC, phenotyping, spatial statistics, and visualisation of single-cell spatial biology data from multiplexed imaging
scimagR	●●○	⧗	End-to-end pipeline for longitudinal MRI/CT analysis in spinal-cord injury research (wraps Spinal Cord Toolbox, dcm2niix)
segmantR	●●○	⧗	Cell segmentation for histology and multiplexed tissue imaging with human-in-the-loop training (classical + Cellpose/StarDist/Mesmer)

Package	Status	DOI	Description
cuvis.r	●●○	⧗	R bindings to the Cubert CUVIS SDK for reading, calibrating, and exporting hyperspectral camera data
hyperspectaculR	●●○	⧗	Publication-grade artistic visualisation of hyperspectral imagery, built on the hyperspectR cube class
hyperspectR	●●○	⧗	Complete pipeline for biomedical hyperspectral imaging — from raw camera data to clinical tissue oxygenation maps
libscanR	●●○	⧗	Vendor-agnostic analysis and visualisation of Laser-Induced Breakdown Spectroscopy (LIBS) data, with a biomedical-tissue focus
tivis.r	●●○	⧗	Pure-R reader for Diaspective Vision TIVITA recordings — no vendor SDK required; companion to cuvis.r

Package	Status	DOI	Description
bambamR	●●○	⧗	Streamlined RNA-seq analysis pipelines — from count matrices to publication-ready results

Package	Status	DOI	Description
molpathR	●●○	⧗	Unified molecular-pathology platform — parses NGS files (VCF, BAM, FASTQ) plus XML/PDF reports and clinical data
zhncommandR	●●○	-na-	Auditor live-evaluation dashboard for haematological oncology cohorts — quality/coverage indicators, OPS-coded complex-therapy and diagnostics counts, Kaplan–Meier, oncoprint, and cytogenetics summaries in an interactive Shiny app

Package	Status	DOI	Description
harbouR	●●○	⧗	Unofficial R client for the SeaTable REST API — read, write, and sync collaborative cloud databases from R
lstparsR	●●○	-na-	Parser for NONMEM .lst output files — extracts THETA / OMEGA / SIGMA estimates into tidy data frames for population PK/PD analysis
pressR	●●○	⧗	Parsing, analysis, and visualisation of capacitive pressure-distribution data (insoles, saddles, seating, pedography)
qviewparsR	●●●		Pure-R parser for the binary .Q-View project format used in chemiluminescent multiplex ELISA plate imaging
researchR	●○○	—	R client for literature and signal surveillance through a separately deployed researchd server; retrieves records and manages surveillance questions.

Package	Status	DOI	Description
dynasimR	●●○	⧗	Domain-neutral analysis and visualisation layer for discrete-event, agent-based, and node-actor simulation outputs
scimapR	●●○	⧗	Reproducible, question-driven, embedding-aware science mapping — bibliometric and scientometric analysis toolkit
songR	●●○	⧗	Native R/C++ implementation of SONG (Self-Organizing Nebulous Growths) for nonlinear dimensionality reduction
inferguidR	●○○	—	Guided inference, power analysis and diagnostic accuracy, with explicit assumptions, typed results, reproducible exports and a Shiny workbench.
sandtablR	●○○	—	Synthetic patient-flow simulation, decision-path analysis and model comparison, with an interactive Shiny workbench.
shieldR	●○○	—	Abstract logistics-chain simulation with time-varying item specifications and dynamic disruptions, with reproducible policy comparisons and a Shiny workbench.

Package	Status	DOI	Description
hexmakR	●●○	⧗	Generate polished hex sticker logos for R packages using customizable templates
reflowR	●●○	⧗	Custom workflowr themes and templates for reproducible research websites in R
themakR	●●○	⧗	Shared pkgdown template giving the CTTIR package suite a unified look — Hugo Coder palette with a light/dark toggle
cttiR	●○○	—	Structured research-project creation, versioned workflow selection and reproducible analysis scaffolding; development software with explicit validation gates.
qupflowR	●○○	—	Experimental R foundations for a planned QuPath interface: protocol helpers, synthetic contract fixtures and pinned external-method execution. Live bridge, interactive app and workflow engine remain planned.

Install implemented CTTIR R packages from their repositories (check each README for requirements):

# install.packages("remotes")
remotes::install_github("CTTIR/<package>")

# lstparsR is maintained in a separate organisation:
# remotes::install_github("Clinical-Pharmacy-Saarland-University/lstparsR")

Standalone apps and tools that complement the R package suite. inferguidR, sandtablR and shieldR also provide Shiny workbenches inside their packages.

Status   ●●● published  ·  ●●○ usable  ·  ●○○ draft  ·  ○○○ idea

Application	Status	DOI	Description
brainwritR	●●○	—	Development R/Shiny application for classroom brainwriting, with timed rounds, QR-code participation, SQLite persistence, mobile reconnect support and German, English and French interfaces.
pwa-quest	●●○	-na-	Offline-first Progressive Web App for collecting questionnaire responses in research and field settings — exports sessions as QR codes or CSV / XLSX / TXT / XML
shinylaunchR	●●○	⧗	Desktop launchpad for package apps, staged Shiny source apps and hosted HTTPS URLs; published 0.1.0 release, with 0.2.0-rc.1 currently an unpublished release candidate
delphyR	●○○	—	Delphi-study platform with R analysis packages, a multilingual Shiny interface and PostgreSQL workflows; synthetic development examples, not a production deployment.
researchd	●○○	—	Self-hosted academic literature and signal surveillance server, with an R pipeline, browser dashboard, token-authenticated API and researchR client.

Plugins that extend Zotero for curated, reproducible reference management.

Status   ●●● published  ·  ●●○ usable  ·  ●○○ draft  ·  ○○○ idea

Plugin	Status	DOI	Description
argus-one	●●○	⧗	Merges duplicate Zotero items by DOI only — keeps the newest record's fields, unions collections, tags, and attachments inside one transaction
attaclone-dedup	●●○	⧗	Detects and resolves duplicate file attachments by content hash — auto-removes byte-identical bare copies, prompts a review dialog for annotated PDFs
metadata-mender	●●○	⧗	Reconciles and completes item metadata against PubMed, OpenAlex, Crossref, Semantic Scholar, OpenAIRE, Unpaywall, CORE, and CRAN

Install by downloading the .xpi from the corresponding repository's Releases page, then Tools → Plugins → ⚙ → Install Plugin From File… in Zotero.

• Organisation website: cttir.github.io/website — source at CTTIR/website

Check each repository for its licence and citation instructions. The new inferguidR, sandtablR, shieldR and researchd public editions use MIT; for R packages, citation("package") reports installed-version metadata. Record the exact version or revision used in an analysis.

For questions, contributions, or collaboration enquiries, open an issue on the relevant repository.

Where applicable, LLM tools were used for narrowly defined, non-authorial tasks: copyediting, prose refinement, Markdown/LaTeX formatting, boilerplate scaffolding (such as CI configurations and build scripts), and code refactoring. Tools included Chat AI, the KISSKI (GWDG) service, and self-hosted Mistral Small (24B, Apache-2.0) served through a local vLLM architecture on an Ubuntu Linux workstation with Intel processors and NVIDIA GPUs. The self-hosted model ran locally, with no data sent to third parties.

All scientific claims, methodological choices, analyses, interpretations and conclusions remain the authors' own. Where applicable, LLM-generated material must be reviewed and revised before inclusion, and references must be verified against their DOI, arXiv ID or ISBN.

Local software setup: vLLM with Python/PyTorch, plus R and RStudio.