roiextractors

v0.5.10

Python module for extracting optical physiology ROIs and traces for various file types and formats For more information about how to use this package see README

Latest version published 2 months ago

License: BSD-3-Clause

PyPI

GitHub

Package Health Score

69 / 100

security
Security review needed
popularity
Small
maintenance
Healthy
community
Sustainable

Popularity

Small

GitHub Stars: 12
Forks: 7
Contributors: 20

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package roiextractors, we found that it has been starred 12 times.

Security

Security review needed

Security and license risk for latest version

Release Date: Nov 6, 2024
Direct Vulnerabilities: 0
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0
H
0
M
0
L
Indirect Vulnerabilities: 0
C
0
H
0
M
0
L
License Risk: 0
H
0
M
0
L

All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

BSD-3-Clause

Security Policy

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Maintenance

Healthy

Commit Frequency

Open Issues: 32
Open PR: 12
Last Release: 2 months ago
Last Commit: 1 month ago

Further analysis of the maintenance status of roiextractors based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Healthy.

We found that roiextractors demonstrates a positive version release cadence with at least one new version released in the past 3 months.

In the past month we didn't find any pull request activity or change in issues status has been detected for the GitHub repository.

Community

Sustainable

Readme: Yes
Contributing.md: No
Code of Conduct: Yes
Contributors: 20
Funding: No

With more than 10 contributors for the roiextractors repository, this is possibly a sign for a growing and inviting community.

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Package

Python Versions Compatibility: >=3.7

Age: 4 years
Latest Release: 2 months ago
Dependencies: 3 Direct / 32 Total
Versions: 19
Maintainers: 0
Wheels: OS Independent

Readme

Full Tests Auto-release

ROIExtractors

Automatically read optical imaging/segmentation data into a common API

Explore our documentation »

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:

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:

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:

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.

roiextractors dependencies

lxml packaging pyyaml

FAQs

What is roiextractors?

Python module for extracting optical physiology ROIs and traces for various file types and formats. Visit Snyk Advisor to see a full health score report for roiextractors, including popularity, security, maintenance & community analysis.

Is roiextractors popular?

The python package roiextractors receives a total of 3,330 weekly downloads. As such, roiextractors popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is roiextractors well maintained?

We found that roiextractors demonstrated a healthy version release cadence and project activity. It has a community of 20 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is roiextractors safe to use?

While scanning the latest version of roiextractors, we found that a security review is needed. A total of 0 vulnerabilities or license issues were detected. See the full security scan results.

Last updated on 20 December-2024, at 16:46 (UTC).

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roiextractors

Python module for extracting optical physiology ROIs and traces for various file types and formats For more information about how to use this package see README

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Package

Readme

ROIExtractors

Automatically read optical imaging/segmentation data into a common API

Table of Contents

About

Installation

Documentation

Funding

License

roiextractors dependencies

FAQs

What is roiextractors?

Is roiextractors popular?

Is roiextractors well maintained?

Is roiextractors safe to use?

Build a secure application checklist

Select a recommended open source package

Scan your app for vulnerabilities

Fix identified vulnerabilities

Monitor for new issues

Package Health Score

Direct Usage Popularity

Security and license risk for latest version

Commit Frequency

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Readme

ROIExtractors

Automatically read optical imaging/segmentation data into a common API

Table of Contents

About

Installation

Documentation

Funding

License

roiextractors dependencies

FAQs

What is roiextractors?

Is roiextractors popular?

Is roiextractors well maintained?

Is roiextractors safe to use?

Build a secure application checklist

Select a recommended open source package

Scan your app for vulnerabilities

Source Code

Open Source

Container

Config

Fix identified vulnerabilities

Monitor for new issues