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_pkgdown.yml
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url: https://natverse.org/fafbseg/
template:
bootstrap: 5
reference:
- title: Package Help
desc: ~
contents:
- '`fafbseg-package`'
- '`dr_fafbseg`'
- '`choose_segmentation`'
- '`simple_python`'
- title: Released FlyWire data
desc: Functions for interacting with the public release data of the FlyWire
whole brain connectome. There are many other useful support / lower level
functions but these are probably the key ones for interacting with release
data.
contents:
- '`download_flywire_release_data`'
- '`flywire_partner_summary2`'
- '`flywire_adjacency_matrix2`'
- '`flywire_ids`'
- '`add_celltype_info`'
- '`flywire_sirepo_file`'
- title: Neuroglancer URLs
desc: Support for generating/parsing Neuroglancer URLs and interconversion of
with FAFB CATMAID URLs and https://flywire.ai
contents:
- '`open_fafb_ngl`'
- '`ngl_encode_url`'
- '`ngl_decode_scene`'
- '`ngl_segments`'
- '`ngl_layers`'
- '`ngl_add_colours`'
- '`ngl_blank_scene`'
- '`flywire_shortenurl`'
- '`flywire_scene`'
- '`ngl_annotations`'
- '`ngl_annotation_layers`'
- '`xform.ngscene`'
- '`voxdims.ngscene`'
- title: FlyWire Neurons
desc: Functions for working with neuron ids, coordinate transforms and
low level functions to talk to a graphene (FlyWire) server.
contents:
- '`flywire_set_token`'
- '`flywire2fafb`'
- '`flywire_voxdims`'
- '`flywire_xyz2id`'
- '`flywire_rootid`'
- '`flywire_latestid`'
- '`flywire_islatest`'
- '`flywire_last_modified`'
- '`flywire_updateids`'
- '`flywire_leaves`'
- '`flywire_change_log`'
- '`flywire_fetch`'
- '`flywire_cloudvolume`'
- '`flywire_l2ids`'
- title: FlyWire Synapses
desc: Functions for working with predicted synapses/neurotransmitters for FlyWire neurons
contents:
- '`flywire_partners`'
- '`flywire_adjacency_matrix`'
- '`flywire_ntpred`'
- '`flywire_ntplot`'
- '`flywire_dcvs`'
- '`flywire_neurons_add_synapses`'
- '`braincircuits_register`'
- '`flywire_connectome_data`'
- title: FlyWire Annotations
desc: Functions for working with FlyWire's own Connectome Annotation Versioning
Engine which is the backend handling all annotations including synapses for
FlyWire and other projects. Alternatively we have our own more flexible flytable system.
contents:
- '`flywire_cave_client`'
- '`flywire_cave_query`'
- '`flywire_timestamp`'
- '`flywire_user_info`'
- '`flywire_nuclei`'
- '`flytable_login`'
- '`flytable-queries`'
- '`flytable_update_rows`'
- '`flytable_list_selected`'
- '`tabify_coords`'
- '`flytable_cell_types`'
- '`flytable_set_celltype`'
- '`fct2nginfo`'
- '`write_nginfo`'
- title: FlyWire Meshes and Skeletons
desc: Functions for working with FlyWire neurons as meshes or skeletons
contents:
- '`read_cloudvolume_meshes`'
- '`read_l2skel`'
- '`meshparty_skeletonize`'
- '`skeletor`'
- '`reroot_hairball`'
- '`fafb14_to_flywire_ids`'
- title: Neuroglancer - CATMAID interconversion
desc: High level approach to converting URLs, neurons etc to representations based
on Neuroglancer / brainmaps data
contents: '`catmaid2ngl`'
- title: FAFB FFN1 segmentation skeletons
desc: Read FAFB FFN1 segmentation skeletons (Peter Li, Google) from packaged zip
files or over the web via brainmaps API.
contents:
- '`read_segments`'
- '`read.neurons.brainmaps`'
- '`read_topn`'
- '`skelsforsegment`'
- '`fafbseg-ids`'
- title: FAFB-FFN1 segmentation agglomeration (merge) information
desc: These functions provide support for loading/using information from the agglomeration
runs that identify candidate merge locations between indiviual raw segment objects.
Some of these merge groups can contain hundreds or even thousands of segments.
Most of the time you will only need find_merged_segments().
contents:
- '`find_merged_segments`'
- '`read_mergeinfo`'
- '`make_merge_graph`'
- '`merge_graph_components`'
- '`find_merged_segments_slow`'
- title: Brainmaps API
desc: Authentication and queries to the Google brainmaps API (what Neuroglancer
talks to under the hood to get image data, segmentation etc).
contents:
- '`brainmaps_auth`'
- '`brainmaps_fetch`'
- '`brainmaps_xyz2id`'
- '`brainmaps_listfragments`'
- '`brainmaps_skeleton`'
- '`read_brainmaps_meshes`'
- '`brainmaps_volume`'
- title: Low level support for Neuroglancer segment meshes
desc: Functions for loading/processing/visualising 3D mesh (wireframe) information
displayed in Neuroglancer. These are low level functions for working with
raw Neuroglancer data. End users may be interested in `compare_ng_neuron`
but otherwise are unlikely to use these.
contents:
- '`compare_ng_neuron`'
- '`fetch_all_curl`'
- '`read_ng_dump`'
- '`read_ng_raw`'
- '`as.mesh3d.ng_raw`'
- '`xyzmatrix.ng_raw`'
navbar:
structure:
left:
- home
- intro
- reference
- articles
- tutorials
- news
- help
right:
- natverse
- github
components:
home:
icon: fa-home fa-lg
href: index.html
reference:
text: Reference
href: reference/index.html
news:
text: Changelog
href: news/index.html
github:
icon: fa-github fa-lg
href: https://github.com/natverse/fafbseg
natverse:
text: natverse
href: https://natverse.org/
help:
text: Help
href: SUPPORT.html