fafbseg

Tools to work with the FlyWire connectome. Fully interoperable with navis.

https://github.com/navis-org/fafbseg-py

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 4 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (11.2%) to scientific vocabulary

Keywords

annotation brain cave connectome fafb fly flywire google navis segmentation synapses

Last synced: 6 months ago · JSON representation

Repository

Tools to work with the FlyWire connectome. Fully interoperable with navis.

Basic Info

Host: GitHub
Owner: navis-org
License: gpl-3.0
Language: Python
Default Branch: master
Homepage: https://fafbseg-py.readthedocs.io
Size: 97.2 MB

Statistics

Stars: 14
Watchers: 2
Forks: 6
Open Issues: 7
Releases: 48

Topics

annotation brain cave connectome fafb fly flywire google navis segmentation synapses

Created over 6 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License

README.md

Tools to work with the FlyWire and Google segmentations of the FAFB EM dataset. Fully interoperable with navis.

Features

Here are just some of the things you can do with fafbseg:

map locations or supervoxels to segmentation IDs
load neuron meshes and skeletons
generate high quality neuron meshes and skeletons from scratch
query connectivity and annotations
parse and generate FlyWire neuroglancer URLs
transform neurons from FAFB/FlyWire space to other brains spaces (e.g. hemibrain)

Documentation

FAFBseg is on readthedocs.

Quickstart

Install latest stable version

bash pip3 install fafbseg -U

Install from Github bash pip3 install git+https://github.com/flyconnectome/fafbseg-py.git

How to cite

If you use fafbseg for your publication, please cite the two FlyWire papers:

"Whole-brain annotation and multi-connectome cell typing quantifies circuit stereotypy in Drosophila" Schlegel et al., bioRxiv (2023); doi: https://doi.org/10.1101/2023.06.27.546055
"Neuronal wiring diagram of an adult brain" Dorkenwald et al., bioRxiv (2023); doi: https://doi.org/10.1101/2023.06.27.546656

Depending on what data you used (e.g. neurotransmitter predictions) you might need to cite additional publications. Please see the Citation Guidelines on Codex.

Owner

Name: NAVis
Login: navis-org
Kind: organization
Location: United Kingdom

Repositories: 10
Profile: https://github.com/navis-org

Tools for Neuron Analysis & Visualization

GitHub Events

Total

Create event: 4
Issues event: 2
Release event: 4
Watch event: 1
Issue comment event: 3
Push event: 9
Pull request review event: 1
Pull request event: 2
Fork event: 1

Last Year

Create event: 4
Issues event: 2
Release event: 4
Watch event: 1
Issue comment event: 3
Push event: 9
Pull request review event: 1
Pull request event: 2
Fork event: 1

Committers

Last synced: about 2 years ago

All Time

Total Commits: 659
Total Committers: 3
Avg Commits per committer: 219.667
Development Distribution Score (DDS): 0.039

Past Year

Commits: 141
Committers: 2
Avg Commits per committer: 70.5
Development Distribution Score (DDS): 0.007

Top Committers

Name	Email	Commits
Philipp Schlegel	o**g@w**e	633
Philipp Schlegel	s****p	24
Eric Perlman	p**n@g**m	2

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 17
Total pull requests: 4
Average time to close issues: 3 months
Average time to close pull requests: 1 day
Total issue authors: 12
Total pull request authors: 4
Average comments per issue: 2.65
Average comments per pull request: 0.75
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 1

Past Year

Issues: 4
Pull requests: 0
Average time to close issues: 4 days
Average time to close pull requests: N/A
Issue authors: 4
Pull request authors: 0
Average comments per issue: 1.75
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

jefferis (3)
schlegelp (3)
masonweinstock (2)
cheongh (1)
dustingarner (1)
liuyx599 (1)
markuspleijzier (1)
michaelfekadu (1)
hubbardp (1)
jialumaomao (1)
JiajunZhang-neu (1)
adjavon (1)

Pull Request Authors

perlman (1)
schlegelp (1)
tomka (1)
dependabot[bot] (1)
DanaSherman (1)

Top Labels

Issue Labels

enhancement (2)

Pull Request Labels

dependencies (1)

Packages

Total packages: 1
Total downloads:
- pypi 270 last-month

Total dependent packages: 1
Total dependent repositories: 1
Total versions: 49
Total maintainers: 1

pypi.org: fafbseg

Tools to work with the FlyWire and Google segmentations of the FAFB EM dataset

Homepage: https://fafbseg-py.readthedocs.io
Documentation: https://fafbseg-py.readthedocs.io
License: GNU GPL V3
Latest release: 3.1.3
published 8 months ago

Versions: 49
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 270 Last month

Rankings

Dependent packages count: 4.8%

Downloads: 11.0%

Average: 13.5%

Forks count: 14.2%

Stargazers count: 16.1%

Dependent repos count: 21.5%

Maintainers (1)

observing

Last synced: 6 months ago

Dependencies

docs/preinstall_requirements.txt pypi

setuptools ==57.5.0

docs/requirements.txt pypi

furo *
ipykernel *
mock *
nbconvert *
nbsphinx *
numpydoc *
sphinx >=3.1
sphinx-autodoc-typehints *

requirements.txt pypi

caveclient *
cloud-volume >=3.1
diskcache *
fastremap *
inquirer >=2.6
ipython *
navis >=0.6.1
numpy *
pandas >=1.1.0
pyarrow >=3.0.0
pyperclip *
python-catmaid >=2.0.2
requests *
requests-futures *
skeletor >=1.0.0
tqdm *
trimesh *

.github/workflows/publish-to-pypi.yml actions

actions/checkout master composite
actions/setup-python v1 composite
pypa/gh-action-pypi-publish master composite

setup.py pypi