fafbseg: Support Functions for Analysis of FAFB EM Segmentation

flywire_rootid

R Documentation

Find the root_id of a FlyWire segment / supervoxel.

Description

Find the root_id of a FlyWire segment / supervoxel.

Usage

flywire_rootid(
  x,
  method = c("auto", "cave", "cloudvolume", "flywire"),
  integer64 = FALSE,
  timestamp = NULL,
  version = NULL,
  cache = FALSE,
  stop_layer = NULL,
  cloudvolume.url = NULL,
  ...
)

Arguments

`x`	One or more FlyWire segment ids
`method`	Whether to use the flywire API (slow but no python required) OR cave/cloudvolume (faster for many input ids, but requires python). "auto" (the default) will choose "cave" or "cloudvolume" (in that order) if available flywire otherwise.
`integer64`	Whether to return ids as integer64 type (more compact but a little fragile) rather than character (default `FALSE`).
`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.
`cache`	Whether to cache supervoxel id -> rootid mappings. Default is `FALSE` and this only works when a `version` or `timestamp` is available. Note that the cache is held in memory and will therefore be regenerated for each R session.
`stop_layer`	Which layer of the chunked graph to stop at. The default `NULL` is equivalent to layer 1 or the full root id. Coarser layer 2 IDs can be a useful intermediate for some operations.
`cloudvolume.url`	URL for CloudVolume to fetch segmentation image data. The default value of NULL chooses the flywire production segmentation dataset.
`...`	Additional arguments passed to `pbsapply` and eventually `flywire_fetch` when `method="flywire"` OR to `cv$CloudVolume` when `method="cloudvolume"`

Details

The main purpose of this function is to convert a supervoxel into the current root id for the whole segment. If a segment id has been updated due to editing, calling with the original segment id will still return the same segment id (although calling it with a supervoxel would return the new segment id). If you wish to find the latest root id, then you can use flywire_latestid, but this is fairly slow (think 1 second per neuron). However in general it is best to select an XYZ location defining a neuron of interest, or the associated supervoxel id and store that, since these can be very rapidly looked up by flywire_xyz2id and flywire_rootid.

There are three methods. "flywire" is simpler but will be much slower for many supervoxels since each id requires a separate http request.

The "cave" method is much faster and can process hundreds of ids per second. In order to avoid sending too many requests in one go (there is a limit to the post message size), id lookups are chunked into a maximum of 50,000 lookups in a single call. This can be modified by passing in the chunksize argument or setting the fafbseg.flywire_roots.chunksize option. Set this smaller if the queries time out / give "Request Entity Too Large" errors. Larger settings are unlikely to have much of a speed impact.

The cloudvolume method was the default until August 2022. It uses the same server endpoint but in my tests is about 2x slower than cave (but still much faster than method='flywire')

Value

A vector of root ids as character vectors.

Examples


flywire_rootid(c("81489548781649724", "80011805220634701"))
# same but using the flywire sandbox segmentation
with_segmentation('sandbox', {
flywire_rootid(c("81489548781649724", "80011805220634701"))
})

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