fafbseg-package: fafbseg: Support Functions for Analysis of FAFB EM...

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

fafbseg: Support Functions for Analysis of FAFB EM Segmentation

Description

Functions that read some of the raw data formats produced by Google electron microscopy segmentation tools as displayed by 'neuroglancer' and then allow basic 3D visualisation and analysis.

Package Options

• fafbseg.sampleurl optionally set to a sample Neuroglancer URL that will modified to point to arbitrary locations by open_fafb_ngl.

• fafbseg.cave.datastack_name optionally set to the datastack_name used by the CAVE system. Expert use only. Normally choose_segmentation looks after this. See flywire_cave_query for further details.

• fafbseg.condaenv the python environment to use with miniconda. Defaults to "r-reticulate", which is the environment set up by reticulate::install_miniconda. You can set this to something different if you would like to keep a separate miniconda virtual environment just for fafbseg (expert use only).

• fafbseg.sqlitepath optional to set the location of SQLite tables used by flywire_partners and friends.

• fafbseg.cachedir The location for disk caches for functions including flywire_leaves If unset on package load, will be set to an appropriate user folder using rappdirs::user_data_dir.

• fafbseg.flcachesize The maximum cache size in bytes. Defaults to 1.5 * 1024^3 when unset. See flywire_leaves for details.

• fafbseg.flywire_roots.chunksize this will default to processing 100,000 rootids at a time. 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. See flywire_rootid for details.

• fafbseg.skelziproot set to the location of a folder containing the zipped versions of the skeletonised segmentations. This will be used by read_segments, read_topn etc.

• fafbseg.skeletonuri a brainmaps URI specifying a remote source used by read.neurons.brainmaps and brainmaps_skeleton to read neuronal skeletons.

• fafbseg.brainmaps_xyz2id.chunksize this will default to querying 4000 vertices at a time. Set this smaller if the queries time out or larger to speed things up. See brainmaps_xyz2id for details.

Author(s)

Maintainer: Gregory Jefferis [e-mail] (ORCID)

Other contributors:

• Sridhar Jagannathan [e-mail] (ORCID) [contributor]

• Alexander Bates [e-mail] (ORCID) [contributor]

See Also

Useful links:

• https://github.com/natverse/fafbseg

• Report bugs at https://github.com/natverse/fafbseg/issues

Examples

options()[grep("^fafbseg\\.", names(options()))]

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