fancr

The goal of fancr is to support analysis of the Female Adult
Nerve Cord dataset aka (FANC), especially autosegmentation data. Those
data are made available by the FANC project led by Wei-Chung Allen Lee (Harvard) and his collaborators including John Tuthill and Sebastian Seung/Zetta.

To access FANC resources, you must have permissions to access the FANC
autosegmentation
dataset
and have confirmed your
acceptance
of the FANC proofreading and data ownership guidelines. At this point you should
have a linked Google account that will be authorised (see below) for access to
FANC online resources.

Broadly speaking the fancr package is a thin wrapper over the
fafbseg package setting up necessary
default paths etc.

Installation

You can install the development version of fancr from github:

if(!requireNamespace('natmanager'))
  install.packages('natmanager')
natmanager::install('natverse', pkgs = 'flyconnectome/fancr')
# install required python packages esp cloudvolume/caveclient
fafbseg::simple_python()

To do anything useful with the fancr package, you need authorisation to access
FANC resources. To prove your authorisation for programmatic access you must
generate and store a token in your web browser after logging in to an approved
Google account. This should be streamlined by running the following command in R
(which will also set you up for Pythonic access via cloudvolume.)

# set up token - will open your browser to generate a new token
fanc_set_token()
# if you already have one do 
# fanc_set_token("<my token>")

To check that everything is set up properly, try:

dr_fanc()
fanc_xyz2id(cbind(34495, 82783, 1954), rawcoords=TRUE)
svids=fanc_leaves("648518346482929060")
head(svids)

Updating

You can just repeat the install instructions, but this ensures
that all dependencies are updated:

natverse::natverse_update(update = T)
natmanager::install(pkgs = 'flyconnectome/fancr')
fafbseg::simple_python()