In natverse/rcatmaid: R access to the API for the CATMAID web image annotation tool

knitr::opts_chunk$set(echo = TRUE)

The Virtual Fly Brain project runs several public CATMAID servers that you can access without any access tokens. This quick example shows you how to access them.

library(dplyr)
library(catmaid)

The vfbcatmaid() function provides a convenient way to connect to those servers.

fafb=vfbcatmaid(dataset = 'fafb')
fafbal=catmaid_get_annotationlist(conn = fafb)
fafbal$annotations %>%
  filter(grepl("^Paper", name))
wang2020a=read.neurons.catmaid('Paper: Wang et al 2020a')
plot(wang2020a, WithNodes=F)

You could do a 3D plot of those neurons

library(elmr)
plot3d(wang2020a)
plot3d(FAFB)

natverse/rcatmaid documentation built on Aug. 19, 2022, 7:52 a.m.