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()