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fafbseg: Support Functions for Analysis of FAFB EM Segmentation

Source: R/fafbseg-package.R
fafbseg-package.Rd

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.

See also

Useful links:

Author

Maintainer: Gregory Jefferis jefferis@gmail.com (ORCID)

Other contributors:

Examples

options()[grep("^fafbseg\\.", names(options()))]
#> $fafbseg.cachedir
#> [1] "/home/runner/.local/share/R/fafbseg"
#> 
#> $fafbseg.cave.datastack_name
#> [1] "flywire_fafb_production"
#> 
#> $fafbseg.cloudvolume.url
#> [1] "graphene://https://prod.flywire-daf.com/segmentation/table/fly_v31"
#> 
#> $fafbseg.condaenv
#> [1] "r-reticulate"
#> 
#> $fafbseg.sampleurl
#> [1] "https://ngl.flywire.ai/#!%7B%22layers%22:%5B%7B%22source%22:%22precomputed://gs://microns-seunglab/drosophila_v0/alignment/image_rechunked%22%2C%22type%22:%22image%22%2C%22blend%22:%22default%22%2C%22shaderControls%22:%7B%7D%2C%22name%22:%22Production-image%22%7D%2C%7B%22source%22:%22graphene://https://prod.flywire-daf.com/segmentation/table/fly_v31%22%2C%22type%22:%22segmentation_with_graph%22%2C%22segments%22:%5B%220%22%5D%2C%22skeletonRendering%22:%7B%22mode2d%22:%22lines_and_points%22%2C%22mode3d%22:%22lines%22%7D%2C%22graphOperationMarker%22:%5B%7B%22annotations%22:%5B%5D%2C%22tags%22:%5B%5D%7D%2C%7B%22annotations%22:%5B%5D%2C%22tags%22:%5B%5D%7D%5D%2C%22pathFinder%22:%7B%22color%22:%22#ffff00%22%2C%22pathObject%22:%7B%22annotationPath%22:%7B%22annotations%22:%5B%5D%2C%22tags%22:%5B%5D%7D%2C%22hasPath%22:false%7D%7D%2C%22name%22:%22Production-segmentation_with_graph%22%7D%5D%2C%22navigation%22:%7B%22pose%22:%7B%22position%22:%7B%22voxelSize%22:%5B4%2C4%2C40%5D%2C%22voxelCoordinates%22:%5B108360%2C42086%2C3279%5D%7D%7D%2C%22zoomFactor%22:8%7D%2C%22perspectiveZoom%22:2230.6094286986126%2C%22jsonStateServer%22:%22https://globalv1.flywire-daf.com/nglstate/post%22%2C%22selectedLayer%22:%7B%22layer%22:%22Production-segmentation_with_graph%22%2C%22visible%22:true%7D%2C%22layout%22:%22xy-3d%22%7D"
#> 
#> $fafbseg.sqlitepath
#> [1] "~/projects/JanFunke/"
#>