Package index • fishr

Overview and setup

fishr fishr-package: fishr: Access the fish2 FlyEM Dataset
fish_setup(): Interactive setup helper for fish2 authentication

Data access

with_fish() choose_fish_dataset() choose_fish(): Evaluate an expression after temporarily setting malevnc options
fish_neuprint(): Login to fish2 neuprint server

Query ids, metadata and connectivity

fish_ids(): Resolve fish2 body ids from a variety of inputs
fish_neuprint_meta(): Fetch neuprint metadata for fish2 neurons
fish_connection_table(): Connectivity query for fish2 neurons
fish_xyz2bodyid(): Map xyz points to fish2 body ids via DVID
register_fish_coconat(): Register fish2 dataset for coconatfly

3D Meshes and Skeletons

fish_rois(): Fetch the ROI hierarchy for fish2
fish_roi_meshes(): Fetch one or more ROI meshes for fish2
read_fish_meshes(): Read meshes for fish2 body ids
read_fish_neurons(): Read neuron skeletons via neuprint

Read and set live annotations

fish_dvid_annotations(): Read DVID body annotations for fish2 body ids
fish_clio_annotations(): Read Clio body annotations for fish2 body ids
fish_annotate(): Set body annotations for fish2 via Clio

Coordinates, spatial transforms and point locations

fish_coords(): Convert xyz points between fish2 coordinate systems
mirror_fish() fish2_mirror_reg: Mirror points or neurons in fish2 space
fish_point_side(): Predict the L/R side of points in fish2 space
fish_somapos() fish_soma_side(): Soma positions and logical sides for fish2 neurons

Utility: URL helpers

reexports flyem_shorten_url flyem_expand_url: Objects exported from other packages