Bioi is an R package containing implementations of solutions to common cell biology image processing problems. In particular, Bioi provides functions to perform connected component labeling on 1, 2, or 3 dimensional arrays, single linkage clustering on n-dimensional arrays, and identification of the points in one data set that are closest to each point in a second data set.
The Bioi project can be found on its GitHub repository. It can be installed from that source using functionality available in the devtools package.
install.packages("devtools")
library(devtools)
install_github("zcolburn/Bioi")
library(Bioi)The objective of single linkage clustering is to place all points into groups such that all points within a group can be reached from any other point in the group by crossing bridges between points that are less than a critical separation distance. A small critical separation distance may result in a larger number of groups being identified. In contrast, a large critical separation distance may result in fewer groups being identified.
Using the function euclidean_linker, single linkage
clustering can be performed in 1 or more dimensions. The function works
in three modes: unpartitioned, partitioned, and parallelized. For small
sample sizes (number of points less than partition_req) the
unpartitioned method is used. For larger sample sizes the partitioned
method is used.
The partitioned method works by iteratively dividing the data into
smaller and smaller subsections until each partition contains fewer
points than partition_req. The unpartitioned method is then
used on each subsection before combining the data from each
subsection.
The parallelized method works similarly to the partitioned method but
operates in parallel. The number of cores to use can be specified by
num_cores. To prevent too many threads from being generated
parallel_call_depth can be specified. A higher depth will
result in more threads being generated.
A common image processing task is to group all connected
“object-positive” pixels in an image into single groups. The connected
component labeling function implemented here can be used on 1, 2, or
3-dimensional arrays representing 1, 2, or 3-dimensional “images”. This
functionality can be accessed using the find_blobs
function.
Photoactivated localization microscopy (PALM) data results in large
numbers of protein localizations being identified. A common task when
working with dual channel PALM data is to identify the distance
separating points in one data set from points in a second data set. The
function find_min_dists identifies the nearest neighbor to
a point in a second data set and its distance from the point of
interest.