jefferis
commented
2 years ago Dear Zhiyong Jiang, thanks for your interest. There is no single account and token – it depends on the dataset that you are hoping to use. If you already have access to a closed access catmaid server, you can get an access token from the catmaid web interface (see http://catmaid.github.io/dev/api.html#api-token).
If not, then you can access some public servers like those from VFB without using a token. The vfbcatmaid() function provides a convenient way to connect to those servers.
library(catmaid)
fafb=vfbcatmaid('fafb')
fafbal=catmaid_get_annotationlist(conn = fafb)
# find annotations that define published papers
library(dplyr)
fafbal$annotations %>%
filter(grepl("^Paper", name))
# get the neurons associated with Wang et al Nature 2020
wang2020a=read.neurons.catmaid('Paper: Wang et al 2020a')
plot(wang2020a, WithNodes=F)
# 3d plot
library(elmr)
plot3d(wang2020a)
plot3d(FAFB)
Hi, I want to use rcatmaid in my research, however, I have no idea where to get an account and the token, could you share the place, I want to apply one. Thank you very much for your help.
All the best, Zhiyong Jiang