flywire_leaves: Find all the supervoxel (leaf) ids that are part of a FlyWire...

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

Find all the supervoxel (leaf) ids that are part of a FlyWire object

Description

This workhorse function underlies the ability to define synaptic connections and neurotransmitter predictions for flywire neurons.

Usage

flywire_leaves(
  x,
  cloudvolume.url = NULL,
  integer64 = FALSE,
  mip = 0L,
  bbox = NULL,
  cache = TRUE,
  ...
)

Arguments

x	One or more FlyWire segment ids
cloudvolume.url	URL for CloudVolume to fetch segmentation image data. The default value of NULL chooses the flywire production segmentation dataset.
integer64	Whether to return ids as integer64 type (the default, more compact but a little fragile) rather than character (when FALSE).
mip	The mip level for the segmentation (expert use only)
bbox	The bounding box within which to find supervoxels (default = NULL for whole brain. Expert use only.)
cache	Whether to cache the results of flywire_leaves calls. See details.
...	Additional arguments passed to pbsapply and eventually flywire_fetch when method="flywire" OR to cv$CloudVolume when method="cloudvolume"

Details

By default repeated calls to flywire_leaves are cached on disk. This functionality is provided by the cachem package now used by the memoise package. By default the cache will expand up to 1.5GB and then start pruning on a least recently used basis (LRU). 1.5GB might store 10-20,000 results for flywire_leaves calls depending on the size of the corresponding neurons.

Since each root id can map to hundreds of thousands of supervoxel ids, there are space implications. In order to save space, the results are stored as compressed 64 bit integers (which are ~30x smaller than character vectors). The compression step does add an extra ~ 5 but is 100x + faster on a cache hit. The default compression is based on the suggested brotli library if available, gzip otherwise.

There is functionality for a memory cache on top of the disk cache, but this is not currently exposed as the disk read time appears small compared with the time for uncompressing and other overheads.

The cache can be controlled by two package options:

• fafbseg.cachedir The location on disk. If not previously set, it is set to an appropriate user folder on package load using rappdirs::user_data_dir. Note that the cache for this function will be located inside a folder called flywire_leaves.

• fafbseg.flcachesize The maximum cache size in bytes. When the storage space exceeds this results are pruned using a LRU algorithm. Defaults to 1.5 * 1024^3 when unset.

Note that the default configuration means that the cache will be shared for a given user across R sessions. It is worth bearing in mind the possibility of race conditions if multiple applications are writing/pruning the cache. For example if the fafbseg.flcachesize has different values in different sessions, the session with the smallest value will start pruning files on disk before the other session.

See Also

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

Examples

kcid="720575940623755722"
length(flywire_leaves(kcid))

## Not run: 
# developer function to check cache status
fafbseg:::flywire_leaves_cache_info()

## End(Not run)

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