Package: vmeasur 0.1.4
vmeasur: Quantify the contractile nature of vessels monitored under an operating microscope
A variety of tools to allow the quantification of videos of the lymphatic vasculature taken under an operating microscope. Lymphatic vessels that have been injected with a variety of blue dyes can be tracked throughout the video to determine their width over time. Code is optimised for efficient processing of multiple large video files. Functions to calculate physiologically relevant parameters and generate graphs from these values are also included.
Authors:
vmeasur_0.1.4.tar.gz
vmeasur_0.1.4.zip(r-4.5)vmeasur_0.1.4.zip(r-4.4)vmeasur_0.1.4.zip(r-4.3)
vmeasur_0.1.4.tgz(r-4.4-any)vmeasur_0.1.4.tgz(r-4.3-any)
vmeasur_0.1.4.tar.gz(r-4.5-noble)vmeasur_0.1.4.tar.gz(r-4.4-noble)
vmeasur_0.1.4.tgz(r-4.4-emscripten)vmeasur_0.1.4.tgz(r-4.3-emscripten)
vmeasur.pdf |vmeasur.html✨
vmeasur/json (API)
| # Install 'vmeasur' in R: |
| install.packages('vmeasur', repos = c('https://jameshucklesby.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jameshucklesby/vmeasur/issues
- example_vessel - Example lymphatic width dataset
Last updated 3 years agofrom:4ece81d4d5. Checks:OK: 6 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 29 2024 |
| R-4.5-win | ERROR | Oct 29 2024 |
| R-4.5-linux | OK | Oct 29 2024 |
| R-4.4-win | OK | Oct 29 2024 |
| R-4.4-mac | OK | Oct 29 2024 |
| R-4.3-win | OK | Oct 29 2024 |
| R-4.3-mac | OK | Oct 29 2024 |
Exports:calibrate_pixel_sizeoutput_dirquantify_directoryquantify_mean_widthquantify_mean_width_sectionsquantify_width_positionscratch_dirselect_roithreshold_applythreshold_vessel
Dependencies:abindaskpassavbackportsbitbit64bmpbootbroomcarcarDataclicliprcodetoolscolorspacecorrplotcowplotcpp11crayoncurlDerivdigestdoBydoFuturedownloaderdplyrfansifarverforeachFormulafuturefuture.applygenericsggplot2ggpubrggrepelggsciggsignifglobalsgluegridExtragtablehmsigraphimagerisobanditeratorsjpeglabelinglatticelifecyclelistenvlme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivparallellypbkrtestpdftoolspillarpkgconfigpngpolynompracmaprettyunitsprogressprogressrpurrrqpdfquantregR6RColorBrewerRcppRcppEigenreadbitmapreadrrlangrstatixrstudioapiscalesSparseMstringistringrsurvivalsvDialogssvGUIsystibbletidyrtidyselecttifftzdbutf8vctrsviridisLitevroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calibrate the pixel size using a test image | calibrate_pixel_size |
| Example lymphatic width dataset | example_vessel |
| Set the output directory | output_dir |
| Quantify the content of an entire directory of sub-directories at once | quantify_directory |
| Quantify the vessel width over an entire ROI | quantify_mean_width |
| Quantify the contractility of a vessel in sections along it's length | quantify_mean_width_sections |
| Quantify the width of a vessel continuously along it's length | quantify_width_position |
| Set the scratch directory for vmeasur | scratch_dir |
| Select a ROI from a video file | select_roi |
| Threshold a video with pre-determined parameters | threshold_apply |
| Apply a threshold to a single frame | threshold_vessel |
