read_mergeinfo: Read CSV files containing raw agglomeration (merge)...

In natverse/fafbseg: Support Functions for Analysis of FAFB EM Segmentation

Read CSV files containing raw agglomeration (merge) information

Description

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

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.

Value

a data.frame with columns

• id1,id2 Segment ids to be merged

• x,y,z Location (in nm) of merge point

See Also

find_merged_segments, fafbsegdata package

Examples

## Not run: 
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)

## End(Not run)

natverse/fafbseg documentation built on Nov. 11, 2024, 9:50 p.m.