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<!DOCTYPE html>
<html lang="en">
<head>
<title>BIAFLOWS: A BioImage Analysis workflows benchmarking platform</title>
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<h1 class="logo">
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<span class="text-highlight">BIA</span><span class="text-bold">FLOWS</span>
</h1>
</div><!--//branding-->
<div class="tagline">
<p>A <span style="color: #fe7f7f;">B</span>io <span style="color: #fe7f7f;">I</span>mage <span style="color: #fe7f7f;">A</span>nalysis workflows benchmarking platform.</p>
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<section class="cards-section text-center">
<div class="container">
<h2 class="title">Getting started is easy!</h2>
<div class="intro">
<p><span style="color:#fe7f7f;">BIA</span>FLOWS is a web platform centralizing Bio Image Analysis (BIA) workflows to automatically extract biological objects annotations from microscopy images. The workflows can be launched online on a predefined set of annotated images illustrating classical BIA problems (e.g. Nuclei segmentation), and the results visualized or quantitatively compared from documented benchmark metrics. To ensure full reproducibility, the workflows are packaged with their execution environments as versioned Docker images compiled from <a class="link" href="user_guide.html#architecture" target="_blank"><span>open source code repositories</span></a>.</p>
<p>Read the <a class="link" href="https://doi.org/10.1016/j.patter.2020.100040" target="_blank"><span>article</span></a>, or browse the following sections to learn more about <span style="color:#fe7f7f;">BIA</span>FLOWS.
</p>
<!--//cta-container-->
</div><!--//intro-->
<div id="cards-wrapper" class="cards-wrapper row">
<div class="item item-green col-lg-4 col-6">
<div class="item-inner">
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<i class="icon fas fa-tachometer-alt"></i>
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<h3 class="title">Benchmarking</h3>
<p class="intro">How to benchmark BIA workflows and why is it critical?</p>
<a class="link" href="https://drive.google.com/file/d/15qBBS6wkNrQWfwGwlBFtrjn0iy5RgXNN/view?usp=sharing" target="_blank"><span></span></a>
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<h3 class="title">Video tutorial</h3>
<p class="intro">Demo on how to use <span style="color:#fe7f7f;">BIA</span>FLOWS online instance</p>
<a class="link" href="https://drive.google.com/open?id=1De8ZilKdcLINaLbmor_B1yDRFWSjfVvg" target="_blank"><span></span></a>
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<h3 class="title">Start</h3>
<p class="intro">Access <span style="color:#fe7f7f;">BIA</span>FLOWS online instance</p>
<a class="link" href="http://biaflows.neubias.org" target="_blank"><span></span></a>
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<h3 class="title">Experiment</h3>
<p class="intro">Access <span style="color:#fe7f7f;">BIA</span>FLOWS sandbox</p>
<a class="link" href="http://biaflows-sandbox.neubias.org" target="_blank"><span></span></a>
</div><!--//item-inner-->
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<h3 class="title">User Documentation</h3>
<p class="intro">A User guide to <span style="color:#fe7f7f;">BIA</span>FLOWS</p>
<a class="link" href="user_guide.html"><span></span></a>
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<h3 class="title">Community forum</h3>
<p class="intro">Where to ask questions and get answers on anything related to <span style="color:#fe7f7f;">BIA</span>FLOWS</p>
<a class="link" href="https://forum.image.sc/tags/biaflows" target="_blank"><span></span></a>
</div><!--//item-inner-->
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<div class="item item-pink item-2 col-lg-4 col-6">
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<i class="icon fas fa-server"></i>
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<h3 class="title">Installing and populating BIAFLOWS locally</h3>
<p class="intro">Install a local <span style="color:#fe7f7f;">BIA</span>FLOWS server to process your own images with public workflows</p>
<a class="link" href="installing_populating_biaflows_locally.html"><span></span></a>
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<h3 class="title">Creating a BIA workflow and adding it to a BIAFLOWS instance</h3>
<p class="intro">Package your own workflow to make it available from <span style="color:#fe7f7f;">BIA</span>FLOWS</p>
<a class="link" href="creating_bia_workflow_and_adding_to_biaflows_instance.html"><span></span></a>
<!--<a class="link" href="assets/pdfs/Creating a BIA workflow and adding it to a BIAFLOWS instance.pdf" target="_blank"><span></span></a>-->
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<i class="icon fas fa-toolbox"></i>
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<h3 class="title">Creating a BIA workflow and adding it to a BIAFLOWS instance (Developer guide)</h3>
<p class="intro">Provide extra information and the procedure to build and debug workflow Docker images locally</p>
<a class="link" href="developer_guide_add_new_workflow_to_biaflows_instance.html"><span></span></a>
<!--<a class="link" href="assets/pdfs/Developer guide to add a new workflow to a BIAFLOWS instance.pdf" target="_blank"><span></span></a>-->
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<i class="icon fas fa-tachometer-alt"></i>
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<h3 class="title">Problem classes, ground truth annotations and reported metrics</h3>
<p class="intro">The different BIA problem classes, computed metrics and annotations encoding</p>
<a class="link" href="problem_class_ground_truth.html"><span></span></a>
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<i class="icon fas fa-cogs"></i>
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<h3 class="title">Executing a BIAFLOWS workflow without BIAFLOWS server</h3>
<p class="intro">Process a folder of local images with a <span style="color:#fe7f7f;">BIA</span>FLOWS workflow</p>
<a class="link" href="executing_biaflows_workflow_without_biaflows_server.html"><span></span></a>
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<i class="icon fas fa-globe"></i>
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<h3 class="title">Access BIAFLOWS from a Jupyter notebook</h3>
<p class="intro">Access BIAFLOWS from a Jupyter notebook to download images and process them (launch Binder from linked GitHub repository)</p>
<a class="link" href="https://github.com/Neubias-WG5/biaflows_jupyter_minimal" target="_blank"><span></span></a>
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<h3 class="title">Install</h3>
<p class="intro">Install your own version of <span style="color:#fe7f7f;">BIA</span>FLOWS</p>
<a class="link" href=""><span></span></a>
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<h3 class="title">Adding new Analysis Workflows</h3>
<p class="intro">Add your own workflow</p>
<a class="link" href=""><span></span></a>
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