Package: BioThermR 0.1.1

BeiHao Li

BioThermR: Standardized Processing and Analysis of Thermal Imaging Data in Animal Studies

A modular framework for standardized analysis of thermal imaging data in animal experimentation. The package integrates thermographic data import (FLIR, raw, CSV), automated region of interest (ROI) segmentation based on 'EBImage' (Pau et al., 2010 <doi:10.1093/bioinformatics/btq046>), interactive ROI refinement, and high-throughput batch processing.

Authors:BeiHao Li [aut, cre]

BioThermR_0.1.1.tar.gz
BioThermR_0.1.1.zip(r-4.7-any)BioThermR_0.1.1.zip(r-4.6-any)BioThermR_0.1.1.zip(r-4.5-any)
BioThermR_0.1.1.tgz(r-4.6-any)BioThermR_0.1.1.tgz(r-4.5-any)
BioThermR_0.1.1.tar.gz(r-4.7-any)BioThermR_0.1.1.tar.gz(r-4.6-any)
BioThermR_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
BioThermR/json (API)

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

Bug tracker:https://github.com/rightsz/biothermr/issues

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

On CRAN:

Conda:

4.78 score 1 stars 306 downloads 28 exports 125 dependencies

Last updated from:e2df98e80f. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develWARNING171
source / vignettesOK238
linux-releaseWARNING188
macos-releaseWARNING225
macos-oldrelWARNING250
windows-develWARNING102
windows-releaseWARNING109
windows-oldrelWARNING111
wasm-releaseOK152

Exports:aggregate_replicatesanalyze_thermal_statsas_EBImageassess_replicatescompile_batch_statscorrelate_thermal_traitscreate_BioThermRfrom_EBImageload_biothermrmerge_clinical_dataplot_roi_overlapplot_thermal_3dplot_thermal_cloudplot_thermal_densityplot_thermal_heatmapplot_thermal_montageread_thermal_batchread_thermal_flirread_thermal_rawroi_filter_interactiveroi_filter_thresholdroi_segment_ebimagesave_biothermrviz_cor_heatmapviz_cor_scatterviz_thermal_barplotviz_thermal_boxplotviz_thermal_montage2

Dependencies:abindaskpassbackportsbase64encBiocGenericsbitopsbootbroombslibcachemcarcarDataclicolorspacecommonmarkcorrplotcowplotcpp11crosstalkcurldata.tableDerivdigestdoBydplyrEBImageevaluatefarverfastmapfftwtoolsfontawesomeforecastFormulafracdifffsgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrisobandjpegjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4lmtestlocfitmagrittrMASSMatrixMatrixModelsmemoisemgcvmimeminqamodelrnlmenloptrnnetnumDerivopensslotelpbkrtestpillarpkgconfigplotlypngpolynompromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasrlangrmarkdownrstatixS7sassscalesshinysourcetoolsSparseMstringistringrsurvivalsysThermimagetibbletidyrtidyselecttifftimeDatetinytexurcautf8vctrsviridisLitewithrxfunxtableyamlzoo

Case Study Demo
Introduction | ⚠️ Important Note: Data Availability | 1. Setup and Installation | 2. Data Loading & Segmentation | 3. Visualization | 4. Statistical Extraction & Compilation | 5. Statistical Comparison | 6. Correlation Analysis | 7. Figure Assembly
Rendered fromBioThermR_case_study.Rmdusingknitr::rmarkdown

Last update: 2026-04-16
Started: 2026-01-13

Quickstart
1. Import Thermal Data | 2. Visualize Raw Data | 3. Automated Segmentation | 4. Calculate Statistics | 5. Batch Processing & Montage | 6. Compile Statistics to Data Frame
Rendered fromQuickStart.Rmdusingknitr::rmarkdown

Last update: 2026-01-11
Started: 2026-01-11

Readme and manuals

Help Manual

Help pageTopics
Aggregate Technical Replicates for Statistical Rigoraggregate_replicates
Calculate Comprehensive Thermal Statisticsanalyze_thermal_stats
Convert BioThermR Object to EBImage Objectas_EBImage
Assess replicate consistency and repeatabilityassess_replicates
Compile Batch Statistics into a Tidy Data Framecompile_batch_stats
Pairwise Correlation Analysis for Thermal and External Traitscorrelate_thermal_traits
Create BioThermR Object from Datacreate_BioThermR
Import EBImage Object into BioThermRfrom_EBImage
Load BioThermR Data from Diskload_biothermr
Merge Thermal Stats with Clinical Datamerge_clinical_data
Visualize ROI Overlap and Dice Coefficientplot_roi_overlap
Interactive 3D Thermal Surface Plotplot_thermal_3d
Generate a "Thermal Cloud" Visualization (Phyllotaxis Layout)plot_thermal_cloud
Visualize Temperature Distribution (Density Plot)plot_thermal_density
Visualize Thermal Matrix as 2D Heatmapplot_thermal_heatmap
Create a Gap-Free Thermal Image Montageplot_thermal_montage
Batch Read .raw Filesread_thermal_batch
Read FLIR Radiometric JPG Fileread_thermal_flir
Read a Single .raw Thermal Image Fileread_thermal_raw
Interactive ROI Selector with Denoising (Shiny App)roi_filter_interactive
Filter Thermal Image by Temperature Thresholdsroi_filter_threshold
Automated ROI Segmentation via EBImageroi_segment_ebimage
Save BioThermR Data Objects to Disksave_biothermr
Visualize Thermal Correlation Heatmapviz_cor_heatmap
Visualize Correlation Scatter Plotviz_cor_scatter
Generate Publication-Ready Comparative Barplotsviz_thermal_barplot
Generate Publication-Ready Comparative Boxplotsviz_thermal_boxplot
Create a Thermal Image Montageviz_thermal_montage2