NBLAST EM tracing against flycircuit (or other databases of) neurons
nblast_fafb(skids, db = NULL, conn = NULL, mirror = TRUE, normalised = TRUE, reverse = FALSE, reference = nat.flybrains::FCWB, .parallel = TRUE, ...)
catmaid_skids
)options('nat.default.neuronlist')
.catmaid
connection object (see
catmaid_connection
)TRUE
since
flycircuit neurons are on fly's left and most FAFB tracings are on fly's
right.)db
contains partial skeletons/tracts; default
FALSE
).templatebrain
object such as FCWB
or a character vector
naming such an object.nblast
for how to use the parallel interface
provided by the doMC
package.)nblast
an object of class nblastfafb for which plot3d
, summary
and hist
methods exist.
Still depends on having a neuronlist
containing
registered neurons (usually from flycircuit.tw). The example code downloads
a set of projection neurons. The full data must be requested from Greg
Jefferis.
When .parallel=TRUE
, nblast_fafb will parallelise the search across
multiple cores if possible. You can set an option specifying a default
number of cores elmr.nblast.cores
. See elmr-package
.
Otherwise the default will either be roughly half the number of cores as
determined by registerDoParallel
. If your machine
does not have multiple cores (or you do not want to use them), the search
will be a bit more efficient if you set the option
elmr.nblast.cores=1
or the argument .parallel=TRUE
.
nblast
,
registerDoParallel
for setting spreading load
across cores.
## Not run: ------------------------------------ # # first load neuronlist object containing registered neurons (see details) # allpndps=flycircuit::load_si_data('allpndps.rds') # # ... and set that as the default for queries and plotting # options(nat.default.neuronlist='allpndps') # # # then make sure you are loged in to catmaid server # # catmaid::catmaid_login(<your connection args>) # # # nblast neuron 27884 # PN27884f=nblast_fafb(27884, mirror = FALSE) # # summary table of results # summary(PN27884f) # # plot results, just top hit # plot3d(PN27884f, hits=1) ## ---------------------------------------------