fafbseg: Support Functions for Analysis of FAFB EM Segmentation

flywire_partners

R Documentation

Find the input/output partners for a flywire neuron

Description

flywire_partners is a low level function returning one row for every synapse.

flywire_partner_summary summarises the connectivity of one or more flywire neurons.

Usage

flywire_partners(
  rootids,
  partners = c("outputs", "inputs", "both"),
  details = FALSE,
  roots = TRUE,
  reference = c("either", "FAFB14", "FlyWire"),
  cloudvolume.url = NULL,
  method = c("auto", "spine", "sqlite"),
  Verbose = TRUE,
  local = NULL,
  ...
)

flywire_partner_summary(
  rootids,
  partners = c("outputs", "inputs"),
  threshold = 0,
  remove_autapses = TRUE,
  cleft.threshold = 0,
  summarise = FALSE,
  surf = NULL,
  version = NULL,
  timestamp = NULL,
  chunksize = NULL,
  method = c("auto", "spine", "sqlite", "cave"),
  Verbose = NA,
  local = NULL,
  ...
)

Arguments

`rootids`	Character vector specifying one or more flywire rootids. As a convenience for `flywire_partner_summary` this argument is passed to `flywire_ids` allowing you to pass in data.frames, flywire URLs or cell type queries.
`partners`	Whether to fetch input or output synapses or both.
`details`	Whether to include additional details such as X Y Z location (default `FALSE`)
`roots`	Whether to fetch the flywire rootids of the partner neurons (default `TRUE`)
`reference`	A character vector or a `templatebrain` object specifying the reference template brain for any 3D coordinate information. The default value of `"either"` will use the natural reference space of the data source (FAFB14 for SQLite tables, FlyWire for the spine service).
`cloudvolume.url`	The segmentation source URL for cloudvolume. Normally you can ignore this and rely on the default segmentation chosen by `choose_segmentation`
`method`	Whether to use a local SQLite database or remote spine service for synapse data. The default `auto` uses a local database when available (45GB but faster).
`Verbose`	Whether to print status messages
`local`	path to SQLite synapse data. Evaluated by `fafbseg:::local_or_google`. Work in progress. Default is to download this data and place it in `~/projects/JanFunke`.
`...`	Additional arguments passed to `pbsapply`
`threshold`	For `flywire_partner_summary` only return partners with greater than this number of connections to the query neuron(s) (default of 0 returns all connections)
`remove_autapses`	For `flywire_partner_summary` whether to remove autapses (defaults to TRUE)
`cleft.threshold`	A threshold for the cleft score calculated by Buhmann et al 2019 (default 0, we have used 30-100 to increase specificity)
`summarise`	(This was never implemented.) Whether to collapse down the results for multiple query neurons into a single entry for each partner neuron.
`surf`	An object defining a 3D ROI inside which the presynaptic position must be located. Can be a `mesh3d` object, or any object which `as.mesh3d` can handle including `hxsurf` and `boundingbox` objects. See `pointsinside` for details.
`version`	Integer materialisation version. The special value of `'latest'` means the most recent materialisation according to CAVE.
`timestamp`	A timestamp to normalise into an R or Python timestamp in UTC. The special value of `'now'` means the current time in UTC.
`chunksize`	(expert use) number of query neurons to send per chunk to cave client. Chunking requests speeds up queries (over sending neurons one a time) while still avoiding row number limits on queries with many neurons.

Details

FIXME behaviour when there are no partners is not well-defined.

Note that there are many duplicated connections in this raw output, false autapses (i.e. the same neuron connected to itself) and other false positives. See Buhmann et al for details and ideas about cleaning up the results.

Also note that the ids returned are of the class integer64 for flywire_partners where there is one row for each synapses/connection; but for flywire_partner_summary where rows report the number of connections between pairs of neurons, they are of type character. This is because the integer64 type is more compact but less robust because it is not a base R type but instead provided by the bit64 package. Some R functions such as sapply strip the class from integer64 vectors, treating them as doubles of a completely different value.

flywire_partners and flywire_partner_summary by default report on the active connectivity state of neurons. At present only flywire_partner_summary allows time travel to historic materialisations using the version or timestamp arguments (see flywire_timestamp for details). This support actually depends on the cave backend (which will automatically be selected when method='auto').

Value

A data.frame with a regtemplate attribute specifying the reference brain space for any xyz points. Columns vary slightly depending on whether data is fetched from spine/ITANNA or a local sqlite database. The more obscure ones include:

prepost When partners = "both" then this column will be present. For any given row (synapse), prepost=1 when the initial query neuron is downstream (postsynaptic) and the partner is upstream.
score came straight from Buhmann et al and is supposed to indicate some confidence score for the predicted synapse.
cleft_score is the more useful one and was a later addition by Stephan Gerhard that asks whether the pre and post synapses are positioned at sensible distances on each side of a cleft defined by a separate neural network from Larissa Heinrich in Stephan Saalfeld’s group.

Examples


pp=flywire_partners("720575940621039145")
head(pp)
class(pp$post_id)


# Note that post_id is of type character
flywire_partner_summary("720575940621039145", partners='out')
flywire_partner_summary("720575940621039145", partners='in')
flywire_partner_summary("720575940621039145")

# summary for neuron at a XYZ location (in this case in raw coordinates)
flywire_partner_summary(flywire_xyz2id(cbind(155682, 58180, 3215),
  rawcoords = TRUE))

## Not run: 
# Use Ctrl+Shift+J to share a flywire scene and then do this to get partner
# summary for that URL
flywire_partner_summary(clipr::read_clip())

cct=flywire_cave_query('cambridge_celltypes', live = T)
dl1.lh=flywire_partner_summary(cct$pt_root_id[grep("DL1", cct$cell_type)],
  surf=subset(elmr::FAFB14NP.surf, "LH_R"))
  # use a rectangular bounding box around LH instead
dl1.lhbb=flywire_partner_summary(cct$pt_root_id[grep("DL1", cct$cell_type)],
  surf=boundingbox(subset(elmr::FAFB14NP.surf, "LH_R")))

## End(Not run)

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