Package: hyperspectR 0.2.0.9000

R. Heller

hyperspectR: Hyperspectral Imaging Analysis for Biomedical Applications

Read, process, analyze, and visualize hyperspectral imaging (HSI) data from Cubert snapshot cameras and standard ENVI/TIFF formats. Provides calibration workflows (dark correction, white reference normalization), spectral preprocessing (Savitzky-Golay smoothing, SNV, MSC, derivatives), dimensionless spectral indices, research hemoglobin fraction fitting, dimensionality reduction (PCA, MNF), pixel classification (SAM, SVM, random forest), and constrained spectral unmixing. Includes an interactive 'shiny' explorer, reproducible batch recipes and grouped evaluation tools. Results are research outputs; clinical or device-specific accuracy is not established by the included synthetic examples.

Authors:R. Heller [aut, cre], V. Forstmeier [aut]

hyperspectR_0.2.0.9000.tar.gz
hyperspectR_0.2.0.9000.zip(r-4.7-any)hyperspectR_0.2.0.9000.zip(r-4.6-any)hyperspectR_0.2.0.9000.zip(r-4.5-any)
hyperspectR_0.2.0.9000.tgz(r-4.6-any)hyperspectR_0.2.0.9000.tgz(r-4.5-any)
hyperspectR_0.2.0.9000.tar.gz(r-4.7-any)hyperspectR_0.2.0.9000.tar.gz(r-4.6-any)
hyperspectR_0.2.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hyperspectR/json (API)

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

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

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

On CRAN:

Conda:

4.51 score 16 scripts 59 exports 30 dependencies

Last updated from:642fc056cd. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK181
source / vignettesOK243
linux-releaseOK206
macos-releaseOK120
macos-oldrelOK135
windows-develOK182
windows-releaseOK205
windows-oldrelOK171
wasm-releaseOK135

Exports:hs_absorbancehs_band_ratiohs_batchhs_beer_lamberths_calibratehs_chromophore_datahs_classify_rfhs_classify_svmhs_clinical_indiceshs_continuum_removalhs_dark_correcths_derivativehs_endmembershs_example_cubehs_example_fileshs_export_pnghs_fix_bad_pixelshs_group_summaryhs_grouped_evaluatehs_mnfhs_mschs_ndihs_npihs_pcahs_plot_clinicalhs_plot_imagehs_plot_indexhs_plot_rgbhs_plot_spectrahs_predicths_processhs_read_cubehs_read_cuberths_read_envihs_read_tiffhs_read_tivitahs_recipehs_resamplehs_roi_polygonhs_roi_recths_roi_statshs_run_apphs_samhs_simulate_cubehs_smoothhs_snvhs_sto2hs_thihs_transformhs_twihs_umaphs_unmix_nnlshs_white_normalizehs_write_envihs_write_tiffhsi_cubescale_color_wavelengthscale_colour_wavelengththeme_hsi

Dependencies:clicpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpatchworkpillarpkgconfigpurrrR6RColorBrewerrlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Getting Started with hyperspectR
Installation | Loading the Package | Creating and Inspecting a Cube | Subsetting | Visualization | RGB Composite | Single Band Image | Mean Spectrum | Computing Tissue Indices | Clinical Panel Display | Interactive Exploration | Next Steps | Citation
Rendered fromhyperspectR.Rmdusingknitr::rmarkdown

Last update: 2026-10-14
Started: 2026-05-04

Cubert Camera Data Workflow
Overview | Step 1: Reading ENVI Data | Step 2: Calibration | Step 3: Preprocessing | Step 4: Computing Indices | Step 5: Saving Results
Rendered fromcubert-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-09-10
Started: 2026-05-04

Research Oxygenation Model Workflow
Overview | Step 1: Load Data | Step 2: Preprocessing | Step 3: Dimensionless Band Ratio | Step 4: Beer-Lambert Chromophore Fitting | Step 5: ROI-Based Statistical Analysis | Step 6: Research Panel | Step 7: PCA for Quality Assessment
Rendered fromintraop-oxygenation.Rmdusingknitr::rmarkdown

Last update: 2026-09-10
Started: 2026-05-04

Research Spectral Indices Explained
Hemoglobin Absorption | Tissue Oxygen Saturation (StO2) | Near-Infrared Perfusion Index (NPI) | Tissue Hemoglobin Index (THI) | Custom Normalized Difference Index | Research Panel
Rendered frombiomedical-indices.Rmdusingknitr::rmarkdown

Last update: 2026-09-10
Started: 2026-05-04

Synthetic Regional Spectral Comparison
Scope | Simulating a Demonstration Scene | Tissue Oxygenation Mapping | Perfusion Assessment | Research Panel Overview | ROI Comparison: Affected vs. Unaffected
Rendered fromcompartment-syndrome.Rmdusingknitr::rmarkdown

Last update: 2026-09-10
Started: 2026-05-04

Readme and manuals

Help Manual

Help pageTopics
Subset an hsi_cube Object[.hsi_cube
Convert hsi_cube to Tibbleas_tibble.hsi_cube
Convert hsi_cube to Data Frameas.data.frame.hsi_cube
Plot an hsi_cube Objectautoplot.hsi_cube
Get Dimensions of an hsi_cubedim.hsi_cube
Convert Reflectance to Absorbancehs_absorbance
Compute an Unscaled Spectral Band Ratiohs_band_ratio
Run and Resume a Manifest of Hyperspectral Recordingshs_batch
Beer-Lambert Chromophore Fittinghs_beer_lambert
Calibrate Raw HSI Data to Reflectancehs_calibrate
Get Chromophore Extinction Coefficient Spectrahs_chromophore_data
Random Forest Pixel Classificationhs_classify_rf
SVM Pixel Classificationhs_classify_svm
Compute All Available Clinical Indiceshs_clinical_indices
Continuum Removalhs_continuum_removal
Apply Dark Current Correctionhs_dark_correct
Spectral Derivativehs_derivative
Extract Endmember Spectra from a Cubehs_endmembers
Get Example HSI Cubehs_example_cube
Write Example ENVI Files to a Temporary Directoryhs_example_files
Export a Single-Band Image as PNGhs_export_png
Detect and Correct Bad Pixelshs_fix_bad_pixels
Summarize Repeated ROI Measurements with Group-Level Uncertaintyhs_group_summary
Evaluate Classification with Entire Groups Held Ouths_grouped_evaluate
Minimum Noise Fraction Transformhs_mnf
Multiplicative Scatter Correctionhs_msc
Compute Normalized Difference Index (General Purpose)hs_ndi
Compute Near-Infrared Perfusion Index (NPI)hs_npi
PCA on Hyperspectral Cubehs_pca
Research HSI Panel Displayhs_plot_clinical
Plot Single-Band Spatial Imagehs_plot_image
Plot Index Map with Clinical Color Scalehs_plot_index
Synthesize RGB Image from Spectral Cubehs_plot_rgb
Plot Spectral Profileshs_plot_spectra
Predict Classes in a New Cube Using a Fitted Classifierhs_predict
Execute a Processing Recipehs_process
Read a Hyperspectral Data Cube from Any Supported Formaths_read_cube
Read a Cubert .cu3s Session Filehs_read_cubert
Read an ENVI Hyperspectral Image Filehs_read_envi
Read a Multi-Channel TIFF Filehs_read_tiff
Read a TIVITA Suite Recordinghs_read_tivita
Define a Reproducible Processing Recipehs_recipe
Resample Spectra to New Wavelength Gridhs_resample
Define Polygon ROIhs_roi_polygon
Define Rectangular ROIhs_roi_rect
Compute ROI Statisticshs_roi_stats
Launch Interactive Hyperspectral Image Explorerhs_run_app
Spectral Angle Mapper Classificationhs_sam
Generate a Synthetic HSI Cube for Testing and Exampleshs_simulate_cube
Savitzky-Golay Spectral Smoothinghs_smooth
Standard Normal Variate Correctionhs_snv
Estimate the Oxygenated Hemoglobin Fraction for Researchhs_sto2
Compute Tissue Hemoglobin Index (THI)hs_thi
Apply a Fitted Spectral Transform to Another Cubehs_transform
Compute Tissue Water Index (TWI)hs_twi
UMAP Embedding of Spectral Datahs_umap
Linear Spectral Unmixing via NNLShs_unmix_nnls
Apply White Reference Normalizationhs_white_normalize
Write an HSI Cube to ENVI Formaths_write_envi
Write an HSI Cube to Multi-Band TIFFhs_write_tiff
Create an HSI Cube Objecthsi_cube
Print an hsi_cube Objectprint.hsi_cube
Wavelength-to-Color Scale for Spectral Plotsscale_color_wavelength scale_colour_wavelength
Summarize an hsi_cube Objectsummary.hsi_cube
Minimalist HSI Themetheme_hsi