vessel-annotation

Annotate blood vessels using a web browser

https://github.com/leomol/vessel-annotation

Science Score: 67.0%

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

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CITATION.cff file
Found 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 2 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Academic email domains
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (10.3%) to scientific vocabulary

Last synced: 9 months ago · JSON representation ·

Repository

Annotate blood vessels using a web browser

Basic Info

Host: GitHub
Owner: leomol
License: gpl-3.0
Language: JavaScript
Default Branch: master
Size: 1.45 MB

Statistics

Stars: 1
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 2

Created over 6 years ago · Last pushed over 3 years ago

Metadata Files

Readme License Citation

Blood vessel annotation tool

Manual outlining of vascular cross-sections using a web browser. The annotation task consists of adjusting a polygonal shape with a fixed number of vertices on the top of the vessel. The user can inspect the time evolution of the vessel and their annotations by freely scrolling through the time-lapse images.

This is a standalone version of the annotation toolbox that allows you to load images, complete the task, and download the results to your computer. An alternative version of this annotation toolbox (not available here) runs on a web server and allows an arbitrary number of annotators to simultaneously complete these tasks directly in the cloud where tasks are automatically and centrally served and stored.

For the study "Astrocytes amplify neurovascular coupling to sustained activation of neocortex in awake mice", the annotation tool was deployed in Amazon Web Services and the tasks (consisting of outlining over 25000 images) were completed by crowdsourcing help from participants from Amazon Mechanical Turk.

Prerequisites

Firefox or Chrome.

Installation

Download and extract repository.
Extract test-data.zip.

Usage

If running locally, open annotation.html with a web browser, otherwise, go to the standalone demo.
Follow the annotation instructions.
When finished, click on Submit to download the results.

Demo

Standalone demo
Video demo 1 and demo 2

Output

The results are downloaded to your computer in JSON format where each line corresponds to an image. The following fields are saved: * folder: name of the selected folder. * name: name of the image completed within folder. * area: area calculated inside the polygon drawn. * vertices: x and y coordinates of each point in the drawing. * polygon: x and y coordinates of each point of the concavehall around the vertices. * height: height of the image presented to the user * assignmentId/hitId/workerId: variables used in the server version of the toolbox to identify assignment, task, and annotator, respectively. * start: when task started. * end: when task ended.

Software license

Owner

Name: Leo
Login: leomol
Kind: user

Repositories: 5
Profile: https://github.com/leomol

Citation (CITATION.cff)

cff-version: 1.2.0
title: "Blood vessel annotation tool"
abstract: "Crowdsource annotation tool for outlining vascular cross-sections"
message: If you use this software, please cite it.
type: software
version: 1.0.0
date-released: 2020-01-16
repository-code: https://github.com/leomol/vessel-annotation
authors:
  - family-names: "Molina"
    given-names: "Leonardo A."
    email: "leonardomt@gmail.com"
    affiliation: "University of Calgary"
    orcid: https://orcid.org/0000-0002-6601-7185

GitHub Events

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Last synced: about 1 year ago

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Total issues: 0
Total pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Total issue authors: 0
Total pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

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

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