This is an R package for various 3D analyses on confocal images of microbial biofilms, microcolonies and communities.
If you use functions in the notebooks Loading and preparing images or Quantification of images please cite: Liu et al. (2017) Low-abundant species facilitates specific spatial organisation that promotes multispecies biofilm formation. Envir. Microbiol.
If you use the co_agg function please cite: Liu et al. (2018)
Micro-scale intermixing; a requisite for stable and synergistic
co-establishment in a four-species biofilm.
ISMEJ
If you use the clumps or occupancy functions please cite: Røder et al.
(2018) Enhanced bacterial mutualism through an evolved biofilm phenotype.
ISMEJ
# devtools has to be installed (install.packages("devtools"))
devtools::install_github("Russel88/RCon3D")
Loading and preparing images, required for all analyses
Co-aggregation and relative positioning
Dynamic sectioning of images in z-direction
Most functions can run in parallel by setting the cores argument. This
will highly speed up analyses, but will also use more memory.
loadIMG Load .tif files and turn them into arrays, and save them as
RDS files ready for downstream analysis
findIMG Find already loaded images in a set directory
smoothIMG Median smooth images
morphIMG Apply mathematical morphology kernel on image
merge_channels Create arrays based on combinations of channels. E.g.
intersects, unions or subtractions
quant Quantifies the number of pixels in each image, for each channel
at each layer.
layer_stand Standardize layers based on fill. Relevant if the bottom
of the specimen is the layer with highest fill
layer_split Splits quantification in Top, Middle and Bottom based on
fill and/or a set number of layers
occupancy Estimates the proportion a (target) channel occupy around a
(focal) channel
co_agg Estimates the co-aggregation between two channels. An
undirected version of occupancy
cross_ratio Estimates the ratio between two channels (targets), at
some distance from a focal channel
create_random Create random images for testing
create_nulls Create image files for the empty spaces in an image, such
that this can be used in the analysis. For example, it can then be
calculated how much empty space there is a around a certain channel with
occupancy
extract_layers With the output from layer_split it makes a list of
what layers to analyze in occupancy, clumps, co_agg and
cross_ratio
xy_splits Splits the image in each xy position and then run an
analysis
clumps Detects and quantifys clumps by aggregating pixels
clumps_plot Plots the output from clumps
An internal function, tiff_to_array, is partly borrowed from
https://github.com/rmnppt/iMage. Furthermore, some of the algorithmic
framework for the co_agg,occupancy and cross_ratio analysis is
also borrowed from this repository.