BIAFLOWS

A Bio Image Analysis workflows benchmarking platform.

Getting started is easy!

BIAFLOWS is a web platform integrating Bio Image Analysis (BIA) workflows extracting annotations from biological objects or features apparent in multidimensional microscopy images. The workflows can be launched online on a predefined set of annotated images illustrating common BIA problems (e.g. Nuclei segmentation from 2D images), and their results can be visualized or quantitatively compared from a set of documented benchmarking metrics. To ensure reproducibility, the workflows are packaged with their complete execution environments as versioned Docker images created from browsable source code repositories.

Benchmarking

How to benchmark BIA workflows and why is it critical?

Video tutorial

Demo on how to use BIAFLOWS online instance

Start

Access BIAFLOWS online instance

User Documentation

A User guide to BIAFLOWS

Community forum

Where to ask questions and get answers on anything related to BIAFLOWS

Installing and populating BIAFLOWS locally

Install a local BIAFLOWS server to process your own images with public workflows

Creating a BIA workflow and adding it to a BIAFLOWS instance

Package your own workflow to make it available from BIAFLOWS

Creating a BIA workflow and adding it to a BIAFLOWS instance (Developer guide)

Provide extra information and the procedure to build and debug workflow Docker images locally

Problem classes, ground truth annotations and reported metrics

The different BIA problem classes, computed metrics and annotations encoding

Executing a BIAFLOWS workflow without BIAFLOWS server

Process a folder of local images with a BIAFLOWS workflow

Access BIAFLOWS from a Jupyter notebook

Access BIAFLOWS from a Jupyter notebook to download images and process them (launch Binder from linked GitHub repository)

BIAFLOWS article

Read the scientific article describing BIAFLOWS