read.neurons.fafb: Read neurons from CATMAID with extra meta-data

In jefferis/elmr: Support for working with light and electron microscopy fly brain data

Read neurons from CATMAID with extra meta-data

Description

Use read.neurons.catmaid to acquire neurons from a CATMAID instance. In addition, include as meta-data certain annotations that these neurons have. To select which annotations appear as entries in the neurons' meta-data, select 'meta-annotations' to appear as the data field. By default, meta-annotations for developmental lineage identities are used, to get the lineage / hemilineage to which a FAFB Drosophila neuron belongs.

Usage

read.neurons.fafb(
  skids,
  meta = c("neuron name", "whimsical name", "cell type", "cell body fiber",
    "ItoLee_Lineage", "ItoLee_Hemilineage", "Hartenstein_Lineage",
    "Hartenstein_Hemilineage", "transmitter", "tracing status", "hemibrain match",
    "synonym", "paper", "citation"),
  sub = ".*:",
  OmitFailures = TRUE,
  batch = FALSE,
  catmaid_get_compact_skeleton = TRUE,
  ...
)

fafb_get_meta(
  skids,
  meta = c("neuron name", "whimsical name", "cell type", "cell body fiber",
    "ItoLee_Lineage", "ItoLee_Hemilineage", "Hartenstein_Lineage",
    "Hartenstein_Hemilineage", "transmitter", "tracing status", "hemibrain match",
    "flywire id", "flywire xyz", "FAFB xyz", "synonym", "paper", "citation"),
  sub = ".*:",
  OmitFailures = TRUE,
  ...
)

Arguments

skids	One or more numeric skeleton ids or a character vector defining a query (see catmaid_skids or examples for the syntax).
meta	a vector of meta-annotations to query. The annotations labelled by these meta-annotations will appear as entries in the data.frame attached to the returned neuronlist.
sub	what to remove from pulled annotations, to clean them up a little. Can be set to "" if you do not wish to remove anything.
OmitFailures	Whether to omit neurons for which FUN gives an error. The default value (NA) will result in nlapply stopping with an error message the moment there is an error. For other values, see details.
batch	numeric, if FALSE or 0 neurons are read from CATMAID without being batched. If a number, neurons are read in batches of size batch. If batch is set to TRUE, a batch size of 1000 is used. This can help overcome server time out errors.
catmaid_get_compact_skeleton	whether to use catmaid::catmaid_get_compact_skeleton or catmaid::read.neurons.catmaid to obtain neuron data. In the former case, connectors and tags are not returned.
...	Additional arguments passed to the catmaid_fetch function

Examples

## Not run: 
# Get some information on a published neuron
## 11519370 was pubished first in Dolan et al. 2019
meta = fafb_get_meta("11519370")

# We can get all of the lineage annotations made in the FAFB dataset
## These come from two different naming schemes, one by Volker Hartenstein
## and another by the groups' of K. Ito and T. Lee.
fafb.neurons.lineage =
read.neurons.fafb("annotation:Lineage_annotated")

## End(Not run)

jefferis/elmr documentation built on Sept. 9, 2023, 1:54 p.m.