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roiextractors

Python-based module for extracting from, converting between, and handling optical imaging data from several file formats. Inspired by SpikeInterface.

https://github.com/catalystneuro/roiextractors

Science Score: 54.0%

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
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 13 committers (7.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Python-based module for extracting from, converting between, and handling optical imaging data from several file formats. Inspired by SpikeInterface.

Basic Info
Statistics
  • Stars: 14
  • Watchers: 5
  • Forks: 10
  • Open Issues: 35
  • Releases: 22
Created over 6 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog License Code of conduct Citation

README.md

PyPI version Full Tests Auto-release codecov documentation License

ROIExtractors

Automatically read optical imaging/segmentation data into a common API

Explore our documentation »

Table of Contents

About

ROIExtractors provides a common API for various optical imaging and segmentation formats to streamline conversion and data analysis. ROI stands for Region Of Interest, which is the region in a set of acquired fluorescence images which the segmentation software has determined as a neuron.

Features:

  • Reads data from 10+ popular optical imaging and segmentation data formats into a common API.
  • Extracts relevant metadata from each format.
  • Provides a handy set of methods to analyze data such as get_roi_locations()

Installation

To install the latest stable release of roiextractors though PyPI, type: shell pip install roiextractors

For more flexibility we recommend installing the latest version directly from GitHub. The following commands create an environment with all the required dependencies and the latest updates:

shell git clone https://github.com/catalystneuro/roiextractors cd roiextractors conda env create roiextractors_env conda activate roiextractors_env pip install -e . Note that this will install the package in editable mode.

Finally, if you prefer to avoid conda altogether, the following commands provide a clean installation within the current environment: shell pip install git+https://github.com/catalystneuro/roiextractors.git@main

Documentation

See our ReadTheDocs page for full documentation, including a gallery of all supported formats.

Funding

ROIExtractors is funded by * Stanford University as part of the Ripple U19 project (U19NS104590). * LBNL as part of the NWB U24 (U24NS120057).

License

ROIExtractors is distributed under the BSD3 License. See LICENSE for more information.

Owner

  • Name: CatalystNeuro
  • Login: catalystneuro
  • Kind: organization
  • Email: hello@catalystneuro.com

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Sharda
    given-names: Saksham
  - family-names: Buccino
    given-names: Alessio Paolo
    orcid: https://orcid.org/0000-0003-3661-527X
  - family-names: Dichter
    given-names: Benjamin
    orcid: https://orcid.org/0000-0001-5725-6910
title: "RoiExtractors"
version: 0.3.1
date-released: 2021-03-06
url: "https://github.com/catalystneuro/roiextractors.git"

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 609
  • Total Committers: 13
  • Avg Commits per committer: 46.846
  • Development Distribution Score (DDS): 0.824
Top Committers
Name Email Commits
weiglszonja w****a@g****m 107
h-mayorquin h****n@g****m 104
Saksham Sharda s****a@g****m 104
Cody Baker 5****D@u****m 83
Ben Dichter b****r@g****m 48
Alessio Buccino a****7@g****m 44
pre-commit-ci[bot] 6****]@u****m 40
CodyCBakerPhD c****d@g****m 25
Saksham Sharda 1****0@u****m 21
Cody Baker c****9@n****u 21
Cody Baker c****d@g****m 9
Szonja Weigl w****a@h****u 2
Yaroslav Halchenko d****n@o****m 1
Committer Domains (Top 20 + Academic)
onerussian.com: 1 hallgato.ppke.hu: 1 nd.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 73
  • Total pull requests: 405
  • Average time to close issues: 9 months
  • Average time to close pull requests: 18 days
  • Total issue authors: 14
  • Total pull request authors: 13
  • Average comments per issue: 2.77
  • Average comments per pull request: 1.84
  • Merged pull requests: 328
  • Bot issues: 0
  • Bot pull requests: 46
Past Year
  • Issues: 20
  • Pull requests: 178
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 7 days
  • Issue authors: 5
  • Pull request authors: 5
  • Average comments per issue: 3.2
  • Average comments per pull request: 1.45
  • Merged pull requests: 140
  • Bot issues: 0
  • Bot pull requests: 9
View more stats
Top Authors
Issue Authors
  • h-mayorquin (30)
  • pauladkisson (10)
  • bendichter (7)
  • CodyCBakerPhD (4)
  • weiglszonja (3)
  • alessandratrapani (3)
  • EricThomson (2)
  • RichieHakim (2)
  • daphnedequatrebarbes (2)
  • rly (1)
  • tuanpham96 (1)
  • alejoe91 (1)
  • mhturner (1)
  • laurelrr (1)
Pull Request Authors
  • h-mayorquin (153)
  • pauladkisson (120)
  • pre-commit-ci[bot] (36)
  • CodyCBakerPhD (29)
  • bendichter (29)
  • weiglszonja (25)
  • alessandratrapani (12)
  • daphnedequatrebarbes (12)
  • github-actions[bot] (7)
  • Saksham20 (2)
  • dependabot[bot] (2)
  • rly (1)
  • RichieHakim (1)
Top Labels
Issue Labels
enhancement (24) discussion (7) refactor (7) bug (7) low priority (6) good first issue (3) documentation (3) API design (1) testing (1) question (1) warnings (1)
Pull Request Labels
testing (18) enhancement (17) refactor (13) bug (8) documentation (7) low priority (7) dependencies (4) github_actions (2) warnings (1) high priority (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 4,719 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 2
  • Total versions: 25
  • Total maintainers: 4
pypi.org: roiextractors

Python module for extracting optical physiology ROIs and traces for various file types and formats

  • Homepage: https://github.com/catalystneuro/roiextractors
  • Documentation: https://roiextractors.readthedocs.io//
  • License: BSD 3-Clause License Copyright (c) 2020, Ben Dichter Consulting All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  • Latest release: 0.6.2
    published 10 months ago
  • Versions: 25
  • Dependent Packages: 1
  • Dependent Repositories: 2
  • Downloads: 4,719 Last month
Rankings
Downloads: 3.1%
Dependent packages count: 3.3%
Average: 9.9%
Dependent repos count: 11.9%
Forks count: 14.3%
Stargazers count: 17.1%
Maintainers (4)
bendichter cbaker9 pauladkisson alessandratrapani
Last synced: 10 months ago

Dependencies

.github/workflows/add-to-dashboard.yml actions
  • leonsteinhaeuser/project-beta-automations v1.2.1 composite
.github/workflows/auto-publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • pypa/gh-action-pypi-publish v1.4.2 composite
.github/workflows/run-tests.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v1 composite
  • s-weigand/setup-conda v1 composite
.github/workflows/update-testing-data.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • s-weigand/setup-conda v1 composite
docs/requirements_doc.txt pypi
  • PyYAML *
  • dill ==0.3.2
  • h5py ==2.9.0
  • jupyter-sphinx *
  • lazy_ops ==0.2.0
  • matplotlib *
  • nbsphinx *
  • notebook *
  • numpy *
  • numpydoc *
  • pynwb *
  • scipy ==1.5.2
  • spikeextractors ==0.9.0
  • tifffile *
  • tqdm ==4.48.2
requirements-full.txt pypi
  • natsort >=8.3.1
  • neuroconv >=0.3.0
  • scanimage-tiff-reader ==1.4.1
  • tifffile >=2018.10.18
requirements-minimal.txt pypi
  • PyYAML *
  • dill >=0.3.2
  • h5py >=2.10.0
  • lazy_ops >=0.2.0
  • psutil >=5.8.0
  • pynwb >=2.0.1
  • scipy >=1.5.2
  • tqdm >=4.48.2
requirements-testing.txt pypi
  • parameterized ==0.8.1 test
  • pytest * test
  • pytest-cov * test
  • spikeextractors >=0.9.10 test
pyproject.toml pypi
setup.py pypi