Man pages for Russel88/RCon3D
Analysis of Confocal Images of Microbial Biofilms

center_of_massFind Center of Mass in images
clumpsFind 3D aggregates/clumps
clumps_distFind distances between 3D aggregates/clumps
clumps_plotPlot 3D aggregates
co_agg3D co-aggregation
create_nullsCreate RDS for all empty pixels
create_randomCreate random image
cross_ratio3D cross-ratio
extract_layersExtract layers
findIMGFind arrays created with 'loadIMG' or 'tiff_to_array'
layer_splitSplit quantification in Top, Middle and Bottom
layer_standTrim and standardize quantification
loadIMGLoad .tif images into R
merge_channelsCreate RDS for a combination of channels
morphIMGApply mathematical morphology kernel on image and save as RDS
occupancy3D Occupancy
quantQuantifies the pixels in images
smoothIMGMedian smooth image and save as RDS
tiff_to_arrayMake Array from .tif file(s)
xy_splitsAnalyses for each xy position
Russel88/RCon3D documentation built on May 24, 2018, 5:54 a.m.