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natverse

9 indexed repositories · View on GitHub

malecns
Access to the latest 'Janelia FlyEM' datasets

R · 646 stars
nat
NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

R · 79 stars
nat.nblast
R package implementing the NBLAST neuron search algorithm, as an add-on for the NeuroAnatomy Toolbox (nat) R package.

R · 18 stars
neuprintr
R client utilities for interacting with the neuPrint connectome analysis service

R · 17 stars
fafbseg
Support functions for analysis of Drosophila connectomes especially the FAFB-FlyWire whole brain

R · 14 stars
coconatfly
Comparative Connectomics of Public and In Progress Drosophila Datasets

R · 11 stars
hemibrainr
Code for working with data from Janelia FlyEM's hemibrain project

R · 9 stars
malevnc
Support for working with Janelia FlyEM Male VNC dataset

R · 3 stars
coconat
Core Connectomics Utilities for the Natverse

R · 2 stars

Beginner friendly Everything

Open All

Fix string NA vs NA in MANC for cf_meta Open

Difficulty 2/5 1-3 hours Newbie friendliness 64/100

natverse/coconatfly#57 · Opened Apr 23, 2026
Improve error message when there is limited connectivity Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

natverse/coconatfly#48 · Opened Dec 19, 2025
coord2ind is memory hungry Open

natverse/nat#521 · Opened Oct 12, 2025
speed up neuprint_get_fields() Open

natverse/neuprintr#183 · Opened Oct 1, 2025
neuprint_fetch_custom(cache=T) misses Open

natverse/neuprintr#181 · Opened Oct 1, 2025
nblast() function returns 0 on self-similarity Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

natverse/nat.nblast#51 · Opened Sep 15, 2025
flywire_dcvs() Request failed [404] Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

natverse/fafbseg#221 · 1 comment · Opened Jun 27, 2025
In mcns_annotate_body protect = TRUE not working Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

natverse/malecns#29 · 1 comment · Opened Feb 6, 2025
normalise query fields Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

natverse/coconatfly#37 · Opened Jan 2, 2025
More uniform fields Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

natverse/coconatfly#29 · 5 comments · Opened Nov 2, 2024
Do not allow creation of new columns when adding annotations to clio so easily Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

natverse/malecns#22 · Opened Oct 9, 2024
Add VNC surface mesh, neuropil mesh and nerves Open

enhancement

natverse/malecns#21 · 4 comments · 1 assignee · Opened Sep 12, 2024
Generic support for additional metadata Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

natverse/coconatfly#23 · 1 comment · Opened Sep 3, 2024
Show warning when ids are dropped because under threshold Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

natverse/coconat#7 · Opened Aug 9, 2024
FlyEM male OpticLobe synapse information Open

natverse/neuprintr#174 · 2 comments · Opened May 31, 2024
dataset_names generates an error Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

natverse/coconat#6 · Opened May 30, 2024
Interactive vs. exported plots differ Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

natverse/coconatfly#9 · 2 comments · Opened Sep 13, 2023
add option to summarise partner neurons Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

natverse/coconatfly#4 · Opened Jun 16, 2023
option not to add details for partners Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

natverse/coconatfly#3 · Opened Jun 16, 2023
function to add metadata to both pre and post-synaptic partners Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

natverse/coconatfly#2 · Opened Jun 16, 2023
The `app` argument of `gs4_auth_configure()` is deprecated Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

natverse/hemibrainr#57 · 5 comments · Opened Apr 17, 2023
Google authentication Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

natverse/hemibrainr#56 · 2 comments · Opened Mar 24, 2023
neuprint_get_shortest_paths returns empty tibble if one of the cells has NULL as name or type Open

natverse/neuprintr#164 · 6 comments · Opened Oct 26, 2022
consider adding a `nid()` function to handle numeric ids Open

question

natverse/nat#505 · 1 comment · Opened Aug 25, 2022
Post fafbseg update - error when querying 'cambridge_celltypes' table in CAVE Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

natverse/fafbseg#161 · 4 comments · Opened Jul 4, 2022
[BUG] in scaling when neurons don't have names Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

natverse/nat.nblast#47 · Opened Jun 17, 2022
Cannot install hemibrainr Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

natverse/hemibrainr#54 · 1 comment · Opened Jun 10, 2022
nlapply to include metadata from data.frame Open

natverse/nat#500 · Opened Jun 9, 2022
Disparities between ROIs in NG and MANC.surf Open

natverse/malevnc#47 · 1 comment · Opened May 25, 2022
Plotting ROI LNp_T1_R from MANC.surf plots neck slice Open

natverse/malevnc#46 · 1 comment · Opened May 25, 2022
Differences in ROI names between neuprint and MANC.surf Open

natverse/malevnc#45 · 3 comments · Opened May 16, 2022
L2cache data Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

natverse/fafbseg#155 · 1 comment · Opened May 12, 2022
flywire_set_token uses old token filename Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

natverse/fafbseg#145 · Opened Feb 10, 2022
Permission issues in Windows when using simple_python Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

natverse/fafbseg#137 · 7 comments · Opened Dec 8, 2021
write neurons save metadata by default Open

natverse/nat#483 · 1 comment · Opened Sep 3, 2021
Add windows build to github actions Open

natverse/nat#478 · 2 comments · Opened Jul 11, 2021
Support for units in nat Open

natverse/nat#470 · 1 comment · Opened Jun 18, 2021
symmetric_manc drops body position Open

natverse/malevnc#16 · 3 comments · Opened Jun 14, 2021
Add MANC symmetric surface Open

natverse/malevnc#11 · 11 comments · Opened Jun 10, 2021
Hemibrain neurons not available in JRCFIB2018F using hemibrain_neurons Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

natverse/hemibrainr#44 · 2 comments · Opened May 5, 2021
Allow nblast to use basic topological information about neurons Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

natverse/nat.nblast#43 · 11 comments · 1 reaction · Opened Apr 10, 2021
hemibrainr::flywire_ids() returns some bad ids Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

natverse/hemibrainr#38 · 1 comment · Opened Mar 31, 2021
Using ngl_add_colours: retain segment order when displaying in flywire Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

natverse/fafbseg#109 · Opened Mar 19, 2021
Have nblast work with Labels in given neuronlist/dotprops objects Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

natverse/nat.nblast#42 · 2 comments · Opened Jan 28, 2021
flywire_ntplot could have two facets, one for axon and another for dendrite Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

natverse/fafbseg#86 · 1 comment · Opened Jan 25, 2021
batch flywire_rootid lookups for faster synaptic partner finding Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

natverse/fafbseg#84 · 1 comment · Opened Jan 24, 2021
Duplication in user_name in flywire_contributions() Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

natverse/hemibrainr#37 · 2 comments · Opened Jan 21, 2021
catch cases where neurons have no supervoxels (or synapses) Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

natverse/fafbseg#75 · 1 comment · Opened Jan 19, 2021
Define seed points for (all) neurons within a region of interest Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

natverse/fafbseg#70 · 1 comment · Opened Jan 15, 2021
consider caching expensive flywire id lookups Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

natverse/fafbseg#67 · 8 comments · Opened Jan 14, 2021

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