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
threshIMGApply thresholding on image and save as RDS
tiff_to_arrayMake Array from .tif file(s)
xy_splitsAnalyses for each xy position
Russel88/RCon3D documentation built on Sept. 9, 2018, 6:55 a.m.