Package: nandb 2.1.1

nandb: Number and Brightness Image Analysis

Calculation of molecular number and brightness from fluorescence microscopy image series. The software was published in a 2016 paper <doi:10.1093/bioinformatics/btx434>. The seminal paper for the technique is Digman et al. 2008 <doi:10.1529/biophysj.107.114645>. A review of the technique was published in 2017 <doi:10.1016/j.ymeth.2017.12.001>.

Authors:Rory Nolan [aut, cre, cph], Luis Alvarez [ctb, cph], Sergi Padilla-Parra [ctb, ths, cph]

nandb_2.1.1.tar.gz
nandb_2.1.1.zip(r-4.7)nandb_2.1.1.zip(r-4.6)nandb_2.1.1.zip(r-4.5)
nandb_2.1.1.tgz(r-4.6-x86_64)nandb_2.1.1.tgz(r-4.6-arm64)nandb_2.1.1.tgz(r-4.5-x86_64)nandb_2.1.1.tgz(r-4.5-arm64)
nandb_2.1.1.tar.gz(r-4.7-arm64)nandb_2.1.1.tar.gz(r-4.7-x86_64)nandb_2.1.1.tar.gz(r-4.6-arm64)nandb_2.1.1.tar.gz(r-4.6-x86_64)
nandb_2.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
nandb/json (API)

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

Bug tracker:https://github.com/rorynolan/nandb/issues

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

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

5.28 score 2 stars 32 scripts 649 downloads 2 mentions 29 exports 64 dependencies

Last updated from:7f1c7dea0f. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK185
linux-devel-x86_64OK233
source / vignettesOK325
linux-release-arm64OK193
linux-release-x86_64OK182
macos-release-arm64OK146
macos-release-x86_64OK368
macos-oldrel-arm64OK119
macos-oldrel-x86_64OK224
windows-develOK216
windows-releaseOK209
windows-oldrelOK180
wasm-releaseOK141

Exports:brightnessbrightness_folderbrightness_imgbrightness_timeseriesbrightness_timeseries_folderbrightness_ts_imgcc_brightnesscc_brightness_foldercc_brightness_imgcc_brightness_timeseriescc_brightness_timeseries_foldercc_brightness_ts_imgcc_numbercc_number_foldercc_number_imgcc_number_timeseriescc_number_timeseries_foldercc_number_ts_imgcross_varcross_var_pillarsmatrix_raster_plotmedian_filternumbernumber_foldernumber_imgnumber_timeseriesnumber_timeseries_foldernumber_ts_imgsmooth_filter

Dependencies:arrayhelpersassertthatautothresholdrbackportsBBmiscbitbit64checkmateclicliprcodetoolscpp11crayondata.tabledetrendrdoParalleldplyrfarverfilesstringsforeachfsgenericsggplot2gluegridExtragtablehmsijtiffisobanditeratorsjsonlitelabelinglifecyclelubridatemagrittrpillarpkgconfigplyrprettyunitsprogresspurrrR6RColorBrewerRcppRcppParallelreadrreshape2rlangS7scalesstrexstringistringrsvUnittibbletidyselecttimechangetzdbutf8vctrsviridisviridisLitevroomwithr

Calculating brightness with single images
Ordinary brightness | The need for detrending | Thresholding | Calculation including thresholding and detrending | Timeseries calculation | Saving Images | Studying the Distribution of Brightnesses
Rendered fromsingle-images.Rmdusingknitr::rmarkdown

Last update: 2025-01-27
Started: 2018-10-30

Batch mode
Batch processing
Rendered frombatch-mode.Rmdusingknitr::rmarkdown

Last update: 2018-10-30
Started: 2018-10-30

Brightness timeseries
Ordinary brightness | A contiguous brightness timeseries | An overlapped brightness timeseries
Rendered frombrightness-timeseries.Rmdusingknitr::rmarkdown

Last update: 2018-10-30
Started: 2018-10-30

Readme and manuals

Help Manual

Help pageTopics
Calculate brightness from image series.brightness
Brightness calculations for every image in a folder.brightness_folder
Create a brightness time-series.brightness_timeseries
Brightness time-series calculations for every image in a folder.brightness_timeseries_folder
Cross-correlated brightness.cc_brightness
Cross-correlated brightness calculations for every image in a folder.cc_brightness_folder
Create a cross-correlated brightness time-series.cc_brightness_timeseries
Cross-correlated brightness time-series calculations for every image in a folder.cc_brightness_timeseries_folder
Cross-correlated number.cc_number
Cross-correlated number calculations for every image in a folder.cc_number_folder
Create a cross-correlated number time-series.cc_number_timeseries
Cross-correlated number time-series calculations for every image in a folder.cc_number_timeseries_folder
Cross-correlated number and brightness image classes.cc-nb-img-classes cc_brightness_img cc_number_img
Cross-correlated number and brightness time series image classes.cc-nb-ts-img-classes cc_brightness_ts_img cc_number_ts_img
Calculate the _cross-variance_ of two vectors.cross_var
Calculate the _cross-variance_ of corresponding pillars of 3d arrays.cross_var_pillars
Make a raster plot of a matrix.matrix_raster_plot
Smooth and median filters with options for handling NAs.median_filter smooth_filter
nandb: Number and brightness in R.nandb-package nandb
Number and brightness image classes.brightness_img nb-img-classes number_img
Number and brightness time series image classes.brightness_ts_img nb-ts-img-classes number_ts_img
Calculate number from image series.number
Number calculations for every image in a folder.number_folder
Create a number time-series.number_timeseries
Number time-series calculations for every image in a folder.number_timeseries_folder