Read CSV files containing raw agglomeration (merge) information

Usage

read_mergeinfo(x, pattern = "10\\.csv$", voxdims = c(16, 16, 40), ...)

Arguments

x: Input directory
pattern: Optional pattern to identify CSV files
voxdims: Optional voxel dimensions to convert raw pixel coordinates into physical (nm) coordinates
...: Additional arguments passed to readr::read_csv

Value

a data.frame with columns

id1,id2 Segment ids to be merged
x,y,z Location (in nm) of merge point

Details

Peter Li provided 10 CSV files with merge information in Aug 2018 against which this function has been tested. This merge information has been processed to identify which groups segments should be merged together in the fafbsegdata package, which can be accessed using the find_merged_segments function.

Examples

if (FALSE) {
csvdir="~/projects/fafbseg/fafb14_v00c_split3xfill2x_merges/ffnreseg16nm_ms1000_md0.02_c0.6_iou0.7/"
mergeinfo <- read_mergeinfo(csvdir)

# Show 3D position of merge locations for a large merge group containing a
# tangential cell (widefield visual interneuron)
tang_segs <- find_merged_segments(22139217567)
tang_mi <- subset(mergeinfo, id1%in% tang_segs | id2 %in%tang_segs)
points3d(xyzmatrix(tang_mi))

# plot brain surface for context
library(elmr)
plot3d(FAFB)
}