flywire_latestid: Find the most up to date FlyWire rootid for one or more input...

In natverse/fafbseg: Support Functions for Analysis of FAFB EM Segmentation

Find the most up to date FlyWire rootid for one or more input rootids

Description

Finds the supervoxel ids for the input rootid and then maps those to their current rootid by simple majority vote.

Usage

flywire_latestid(
  rootid,
  sample = 100L,
  level = 2L,
  timestamp = NULL,
  version = NULL,
  cloudvolume.url = NULL,
  Verbose = FALSE,
  method = c("auto", "leaves", "cave"),
  ...
)

Arguments

rootid	One ore more FlyWire rootids defining a segment (in any form interpretable by ngl_segments)
sample	An absolute or fractional number of supervoxel ids to map to rootids or FALSE (see details).
level	The resolution level of the chunked graph to use when calculating identity changes. An integer between 1 and 2. The default (2, implying slightly larger supervoxels) is considerably faster but gives good results for all but the smallest fragments. See flywire_l2ids.
timestamp	An optional timestamp as a string or POSIXct, interpreted as UTC when no timezone is specified.
version	An optional CAVE materialisation version number. See details and examples.
cloudvolume.url	URL for CloudVolume to fetch segmentation image data. The default value of NULL chooses the flywire production segmentation dataset.
Verbose	When set to TRUE prints information about what fraction of
method	"cave" uses the caveclient python module, which is generally faster, but has the disadvantage that it does not disambiguate between the two options after a split. For this reason, method="auto" (the default) currently chooses "leaves". NB this method does benefit from the persistent cache in flywire_leaves so second lookups will be much faster.
...	Additional arguments passed to flywire_leaves

Details

By default a sample of the input rootids is used since that step is the most time consuming part. The sample can be defined as a fraction (0<sample<1) or an absolute number. They will be clamped to the actual number of supervoxels in the object.

flywire_latestid does a precheck to see if the input rootids have been updated using flywire_islatest; this precheck is very fast (thousands of neurons per second). Only those ids that are not up to date are then further processed to identify the new rootid. This second step is slow (order 1-10 s per object). If you need to do this regularly for a set of neurons, it is much better to keep an XYZ location or even better a supervoxel id at a safe location on the neuron such as the primary branch point (typically where the cell body fibre joins the rest of the neuron).

Note that after edits that remove pieces of a starting neuron, flywire_latestid will return the id of the largest resultant piece.

Value

A character vector of rootids. When the input is 0 or NA or a rootid that does not exist in the chunked graph, the output will be 0.

See Also

Other flywire-ids: flywire_islatest(), flywire_last_modified(), flywire_leaves(), flywire_rootid(), flywire_updateids(), flywire_xyz2id()

Examples

# one of the neurons displayed in the sandbox
with_segmentation('sandbox', flywire_latestid('720575940625602908'))
## Not run: 
with_segmentation('sandbox', flywire_latestid('720575940625602908', Verbose = T))

# check every supervoxel (slow for bigger neurons, but this KC is smallish)
flywire_latestid('720575940616243077', sample=FALSE)

# update a neuroglancer URL with the most up to date segment ids
# nb this is slow since it looks at all supervoxels - much more efficient to
# store a single xyz location or supervoxel id
u="https://ngl.flywire.ai/?json_url=https://globalv1.flywire-daf.com/nglstate/5695907068641280"
ngl_segments(u) <- flywire_latestid(ngl_segments(u))
# open modified URL in your browser
browseURL(u)


## End(Not run)

natverse/fafbseg documentation built on Nov. 11, 2024, 9:50 p.m.