cellfinder

Automated 3D cell detection in very large images

https://github.com/brainglobe/cellfinder

Science Score: 67.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
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
○
Academic publication links
✓
Committers with academic emails
2 of 12 committers (16.7%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.7%) to scientific vocabulary

Keywords

cell-detection deep-learning image-analysis imaging microscopy neuroanatomy neuroscience python

Keywords from Contributors

atlases brain registration visualisation animal behavior behaviour ethology kinematics motion-tracking

Last synced: 6 months ago · JSON representation ·

Repository

Automated 3D cell detection in very large images

Basic Info

Host: GitHub
Owner: brainglobe
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://brainglobe.info/documentation/cellfinder/index.html
Size: 167 MB

Statistics

Stars: 216
Watchers: 15
Forks: 63
Open Issues: 72
Releases: 35

Topics

cell-detection deep-learning image-analysis imaging microscopy neuroanatomy neuroscience python

Created about 6 years ago · Last pushed 7 months ago

Metadata Files

Readme License Citation

cellfinder

cellfinder is software for automated 3D cell detection in very large 3D images (e.g., serial two-photon or lightsheet volumes of whole mouse brains). There are three different ways to interact and use it, each with different user interfaces and objectives in mind. For more details, head over to the documentation website.

At a glance:

There is a command-line interface called brainmapper that integrates with brainreg for automated cell detection and classification. You can install it through brainglobe-workflows.
There is a napari plugin for interacting graphically with the cellfinder tool.
There is a Python API to allow users to integrate BrainGlobe tools into their custom workflows.

Installation

You can find the installation instructions on the BrainGlobe website, which will go into more detail about the installation process if you want to minimise your installation to suit your needs. However, we recommend that users install cellfinder either through installing BrainGlobe version 1, or (if you also want the command-line interface) installing brainglobe-workflows.

```bash

If you want to install all BrainGlobe tools, including cellfinder, in a consistent manner with one command:

pip install brainglobe>=1.0.0

If you want to install the brainmapper CLI tool as well:

pip install brainglobe-workflows>=1.0.0 ```

If you only want the cellfinder package by itself, you can pip install it alone:

bash pip install cellfinder>=1.0.0

Be sure to specify a version greater than version v1.0.0 - prior to this version the cellfinder package had a very different structure that is incompatible with BrainGlobe version 1 and the other tools in the BrainGlobe suite. See our blog posts for more information on the release of BrainGlobe version 1.

Seeking help or contributing

We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the contact page of our website.

Citation

If you find this package useful, and use it in your research, please cite the following paper:

Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M. and Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets’ PLOS Computational Biology, 17(5), e1009074 https://doi.org/10.1371/journal.pcbi.1009074

If you use this, or any other tools in the brainglobe suite, please let us know, and we'd be happy to promote your paper/talk etc.

Owner

Name: BrainGlobe
Login: brainglobe
Kind: organization
Location: London/Munich

Website: https://brainglobe.info/
Twitter: brain_globe
Repositories: 28
Profile: https://github.com/brainglobe

Open python tools for morphological analyses in systems neuroscience

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: cellfinder
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Adam
    family-names: Tyson
    email: hello@brainglobe.info
    affiliation: 'Sainsbury Wellcome Centre, University College London'
  - given-names: Christian
    family-names: Niedworok
  - given-names: Charly
    family-names: Rousseau
  - given-names: BrainGlobe
    family-names: Developers
    email: hello@brainglobe.info
repository-code: 'https://github.com/brainglobe/cellfinder'
url: 'https://brainglobe.info'
abstract: >-
  Automated 3D cell detection in very large 3D images (e.g.,
  serial two-photon or lightsheet volumes of whole mouse
  brains).
license: BSD-3-Clause
date-released: '2024-01-05'
year: 2024
preferred-citation:
  type: article
  authors:
  - given-names: Adam
    family-names: Tyson
    affiliation: 'Sainsbury Wellcome Centre, University College London'
  - given-names: Charly V.
    family-names: Rousseau
  - given-names: Christian J.
    family-names: Niedworok
  - given-names: Sepiedeh
    family-names: Keshavarzi
  - given-names: Chryssanthi
    family-names: Tsitoura
  - given-names: Lee
    family-names: Cossell
  - given-names: Molly
    family-names: Strom
  - given-names: Troy W.
    family-names: Margrie
  doi: "10.1371/journal.pcbi.1009074"
  url: "https://doi.org/10.1371/journal.pcbi.1009074"
  journal: "PLOS Computational Biology"
  month: 5
  year: 2021
  title: "A deep learning algorithm for 3D cell detection in whole mouse brain image datasets"
  issue: 5
  volume: 17
  pages: 1-17
citation-sentence: "This work makes use of the cellfinder detection algorithm,"

GitHub Events

Total

Create event: 28
Release event: 7
Issues event: 40
Watch event: 38
Delete event: 18
Issue comment event: 224
Push event: 38
Pull request review comment event: 49
Pull request review event: 84
Pull request event: 108
Fork event: 29

Last Year

Create event: 28
Release event: 7
Issues event: 40
Watch event: 38
Delete event: 18
Issue comment event: 224
Push event: 38
Pull request review comment event: 49
Pull request review event: 84
Pull request event: 108
Fork event: 29

Committers

Last synced: over 2 years ago

All Time

Total Commits: 313
Total Committers: 12
Avg Commits per committer: 26.083
Development Distribution Score (DDS): 0.323

Past Year

Commits: 30
Committers: 5
Avg Commits per committer: 6.0
Development Distribution Score (DDS): 0.567

Top Committers

Name	Email	Commits
Adam Tyson	a**n@u**k	212
Adam Tyson	c**e@a**m	58
David Stansby	d**y@g**m	13
pre-commit-ci[bot]	6****]	13
paddyroddy	p**y@g**m	4
Adam Tyson	a**1@i**k	4
Will Graham	3****1	3
Anna Medyukhina	3****a	2
Emanuele Paoli	e**p@g**m	1
Stephen Lenzi	s**i@g**m	1
stegiopast	5****t	1
Niko Sirmpilatze	n**e@g**m	1

Committer Domains (Top 20 + Academic)

icr.ac.uk: 1 adamltyson.com: 1 ucl.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 204
Total pull requests: 250
Average time to close issues: 9 months
Average time to close pull requests: 8 days
Total issue authors: 39
Total pull request authors: 29
Average comments per issue: 2.1
Average comments per pull request: 1.7
Merged pull requests: 174
Bot issues: 0
Bot pull requests: 32

Past Year

Issues: 29
Pull requests: 124
Average time to close issues: about 1 month
Average time to close pull requests: 9 days
Issue authors: 9
Pull request authors: 22
Average comments per issue: 1.48
Average comments per pull request: 2.1
Merged pull requests: 60
Bot issues: 0
Bot pull requests: 17

View more stats

Top Authors

Issue Authors

adamltyson (76)
alessandrofelder (44)
dstansby (20)
cindy12-gao (7)
willGraham01 (7)
IgorTatarnikov (6)
matham (5)
sfmig (4)
Eddymorphling (4)
atranvan (3)
JuiceJenner (2)
larsrollik (2)
viktorpm (2)
jjtukker (1)
JuiceSackey (1)

Pull Request Authors

adamltyson (71)
pre-commit-ci[bot] (39)
IgorTatarnikov (36)
matham (28)
alessandrofelder (24)
sfmig (20)
0Anshu1 (20)
dstansby (14)
parharti (12)
willGraham01 (11)
K-Meech (6)
ayush2281 (6)
paddyroddy (4)
DavidRZ-ai (4)
nischitkumar (4)

Top Labels

Issue Labels

enhancement (99) bug (62) cellfinder-napari (42) cellfinder-core (39) help wanted (12) good first issue (8) documentation (5) question (3) HIGH PRIORITY (2)

Pull Request Labels

CI (3) enhancement (2) bug (1)

Packages

Total packages: 2
Total downloads:
- pypi 1,974 last-month

Total dependent packages: 3
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 154
Total maintainers: 1

proxy.golang.org: github.com/brainglobe/cellfinder

Documentation: https://pkg.go.dev/github.com/brainglobe/cellfinder#section-documentation
License: bsd-3-clause
Latest release: v1.7.0
published 9 months ago

Versions: 43
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 9.0%

Average: 9.6%

Dependent repos count: 10.2%

Last synced: 7 months ago

pypi.org: cellfinder

Automated 3D cell detection in large microscopy images

Homepage: https://brainglobe.info/documentation/cellfinder/index.html
Documentation: https://brainglobe.info/documentation/cellfinder/index.html
License: BSD-3-Clause
Latest release: 1.7.0
published 9 months ago

Versions: 111
Dependent Packages: 3
Dependent Repositories: 0
Downloads: 1,974 Last month

Rankings

Dependent packages count: 3.1%

Downloads: 7.2%

Average: 26.0%

Dependent repos count: 67.6%

Maintainers (1)

alessandrofelder

Last synced: 7 months ago

Dependencies

.github/workflows/test_and_deploy.yml actions

actions/checkout v2 composite
actions/setup-python v1 composite
brainglobe/actions/lint v1 composite
brainglobe/actions/test v1 composite
docker/build-push-action ad44023a93711e3deb337508980b4b5e9bcdc5dc composite
docker/login-action f054a8b539a109f9f41c372932f1ae047eff08c9 composite
docker/metadata-action 98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 composite

pyproject.toml pypi

brainglobe-utils >=0.2.5
brainreg *
cellfinder-core >=0.2.4
configobj *
fancylog >=0.0.7
imio *
multiprocessing-logging >=0.3.4
natsort *
numpy *
packaging *
pandas *
scikit-image *
tifffile *
tqdm *

.github/workflows/test_include_guard.yaml actions

actions/checkout v3 composite
actions/setup-python v4 composite
jannekem/run-python-script-action v1 composite

cellfinder

Science Score: 67.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

cellfinder

Installation

If you want to install all BrainGlobe tools, including cellfinder, in a consistent manner with one command:

If you want to install the brainmapper CLI tool as well:

Seeking help or contributing

Citation

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

proxy.golang.org: github.com/brainglobe/cellfinder

Rankings

pypi.org: cellfinder

Rankings

Maintainers (1)

Dependencies