fishr: Access the Fish2 FlyEM Dataset

A thin wrapper around the malevnc package providing access to the fish2 larval zebrafish EM dataset being proofread at Janelia Research Campus as part of a collaboration with the Engert / Lichtman labs at Harvard and Google Research. Currently provides convenience functions for reading meshes and setting dataset options.

Package Options

• fishr.dataset The name of the active fish2 dataset (default "fish2"). Set by choose_fish_dataset.

The following malevnc.* options are set by choose_fish or with_fish to point the malevnc package at the fish2 servers:

• malevnc.server DVID server URL (set via Clio lookup).

• malevnc.rootnode DVID root node UUID (set via Clio lookup).

• malevnc.neuprint neuprint server URL (fallback: https://neuprint-fish2.janelia.org).

• malevnc.neuprint_dataset neuprint dataset name (fallback: "fish2").

See also

Useful links:

• https://flyconnectome.github.io/fishr/

Other setup-data-access: fish_neuprint(), fish_setup(), with_fish()

Author

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

Examples

if (FALSE) { # \dontrun{
options()[grepl("^fishr", names(options()))]
options()[grepl("^malevnc", names(options()))]
with_fish(read_fish_meshes(12345))
} # }