Releases: natverse/fafbseg
Releases · natverse/fafbseg
v0.9.4
What's Changed
- Add
flywire_updateids()
by @jefferis in #127 - add support for the Seung/Allen python CAVE including
flywire_cave_client()
flywire_cave_query()
(#122) - add
flywire_updateids()
(#127) - also more robustness to handling of NAs in
flywire_rootid()
- first implementation of
flytable_*
functions includingflytable_query()
flytable_list_rows()
flytable_login()
(#126) - note about SSL certificate problem with some flywire/fanc queries bug (#125)
- Add ids type info to
flywire_partners()
New Contributors
Full Changelog: v0.9.3...v0.9.4
v0.9.3
v0.9.2
What's Changed
- Flywire synapse fixes by @alexanderbates in #112
- fix path of cv secret when no domain 3d0a6d2
- Add
flywire_scene()
function b4cf8be
Full Changelog: v0.9.1...v0.9.2
v0.9.1
What's Changed
- Feature/ngscene basic manipulation by @jefferis in #58
- Feature/nglayer manipulation by @jefferis in #60
- Feature/autosyn by @jefferis in #63
- Feature/cache flywire leaves by @jefferis in #71
- Feature/local db path by @jefferis in #73
- Feature/flywire partners both by @jefferis in #77
- Feature/check for raw coords by @jefferis in #82
- Feature/more 64bit ids by @jefferis in #87
- Feature/neuron synapses by @jefferis in #80
- Return errors as warning with tryCatch by @alexanderbates in #90
- Basic implementation of flywire_islatest by @jefferis in #89
- Add optional timestamp to islatest by @jefferis in #92
- Feature/rootid speedups by @jefferis in #93
- Feature/neuroglancer colour by @SiqiFang in #91
- remove two stage travis test as seems to duplicate build by @jefferis in #96
- Feature/persistent cache by @jefferis in #98
- Feature/simpler pyinstall by @jefferis in #99
- Add flywire_adjacency_matrix by @jefferis in #95
- Created flywire_synapse_annotations by @alexanderbates in #100
- Feature/save cloudvolume meshes by @jefferis in #102
- fix flywire_partner_summary when neurons have no synapses by @jefferis in #105
- Warn when trying to fetch synapse details from spine by @jefferis in #106
- Chunk flywire_rootid lookups by @jefferis in #111
- Feature flywire_shortenurl and flywire_expandurl by @jefferis in #113
- Standard github actions setup by @jefferis in #115
- Feature/spine locations by @jefferis in #114
- Skeletor 1.0.0 by @jefferis in #116
- Add support for multiple cave/zetta tokens by @jefferis in #119
New Contributors
Full Changelog: v0.9...v0.9.1
fafbseg v0.8.2
- Much faster
flywire_xyz2id()
supervoxel id mapping using spine service (#44) - Add new
flywire_leaves()
function to find supervoxels in a neuron (#43) - Fixing typos and adding doi for TEASAR (#41 by @mmc46)
- Fixing 2 things in overlay mesh+skeleton example
(#40 by @mmc46) - Fix flywire_xyz2id eg in doc 'The natverse and flywire meshes' returns an error (#39)
- Output of dr_fafbseg() points to wrong token helper function (#38 by @mmc46)
You can see the full list of closed issues
on GitHub.
fafbseg v0.8.1
This release includes changes from both version 0.8.1 and version 0.8.0 (which was never released)
fafbseg 0.8.1
- New function
skeletor()
to skeletonise meshes especially flywire neurons
based on the Python package of the same name (#35). - Large speed up for
flywire_rootid()
(#37) - Fix
flywire_xyz2id()
so that it can actually find supervoxels (as well as root ids) (#37) - function
dr_fafbseg()
to give a status update on your installation (#36) read_cloudvolume_meshes()
can now accept flywire URLs (which will be expanded if necessary to define the segments to download)
fafbseg 0.8.0
- Support for some basic flywire API calls #31, #34
- Better integrate flywire api features
- Fix/flywire coordinate errors
- Fix error in fafb2flywire during xform_brain #30, #32, #33
- Switch to transform-service API on spine
- Add support for FANC3-FANC4 transforms #28
- switch back to wire3d #27
- Add fafb2flywire i.e. the inverse of the original FlyWire->FAFB transformation #26
- Support for reading flywire meshes without cloudvolume #25
- Flywire API streamlining (@SridharJagannathan) #22
- Teach read_cloudvolume_meshes to work for flywire URLs #20
ngl_segments()
needs to be able to expand flywire URLs #16
You can see the full list of closed issues
for the combined 0.8.0 and 0.8.1 release on GitHub.
fafbseg v0.7.0
fafbseg 0.7.0
- basic support for reading meshes via CloudVolume e.g. to fetch neurons from
flywire.ai. Seeread_cloudvolume_meshes()
for details including the required
Python setup. - very basic support for skeletonising neurons meshed (e.g. flywire neurons)
viameshparty_skeletonize()
- add
flywire2fafb()
to support for transforming neurons FlyWire->FAFB
(and with some loss of accuracy in the reverse) (#11) - includes a fix for NaN values in return (#12,#13)
- much faster FlyWire->FAFB transformation, up to millions of points per minute
(#24) - moved repo to https://github.com/natverse/fafbseg (#19)
fafbseg 0.6.5
- default chunksize for
brainmaps_xyz2id()
reduce to 200 to reflect API
changes. - new functions
choose_segmentation()
andwith_segmentation()
to choose
default auto-segmentation - New Shiny app (see README and https://jefferislab.shinyapps.io/CATMAID-Neuroglancer-Converter/)
- give
brainmaps_fetch()
a generic cache option and the ability to clear the
cache withbrainmaps_clear_cache()
(#8) - give
brainmaps_fetch()
a retry option to help with sporadic timeouts (#9) - give
catmaid2ngl()
a chunksize option that can be used to reduce timeout
issues. - simplify package
.onLoad
and retire fafbseg.divisor option
(now calculated automatically rather than being a user option) - simplify internal
brainmaps_voxdims
function using cache mechanism
fafbseg 0.6.4
- fix bug revealed by latest public version of zip package
- fix missing import of
dplyr::n()
infind_topn()
fafbseg 0.6.3
- Give
find_topn()
andread_top()
ability to return segments in
increasing (rather than decreasing) size order.