Bilayers is an open-source specification designed to characterize software containers in terms of expected inputs, expected outputs, and tunable parameters. Its primary aim is to make bioimage analysis deep-learning algorithms more accessible by automatically generating intuitive, no-terminal-required user interfaces. Bilayers ensures that software containers can be deployed consistently across different environments, from small prototypes to large-scale workflows, without the risk of version mismatch.
Bilayers currently supports interfaces like Gradio and Jupyter Notebook and plans to expand to others, such as CellProfiler plugins. Each algorithm-interface pair is containerized and published as a Docker image on DockerHub, allowing users to run the tool effortlessly by spinning up a Docker container. You can start using it right away — No Coding or Complicated Installations needed!
In addition to using pre-built Docker images provided by Bilayers, you can also create your own web interface or Jupyter Notebook interface for custom deep-learning algorithms. You can even fine-tune algorithms from the BioImage Model Zoo by simply filling out a configuration file (as long as the algorithm’s Docker image is available on DockerHub). Bilayers offers a simple, interactive interface with widgets like number inputs, text fields, radio buttons, dropdown menus, image upload options and more. This makes it easy to tweak parameters and input your images for analysis, giving you the desired output with minimal effort.
It ensures that the same containerized algorithms used in prototypes can be reliably deployed in large-scale workflows without version drift, whether on local machines, high-performance computing (HPC) systems, or in the cloud. This also helps sysadmins create and validate workflows for end users in tools like Nextflow or Snakemake.
Bilayers is open-source, and we welcome contributions! You can create an interface for your custom deep-learning algorithm using Bilayers, and if you’d like, we can publish it on DockerHub to benefit the broader bioimaging community.
What are containers?¶
Containers are lightweight piece of software that contains all the code, libraries, and dependencies that the application needs to run. Containers do not have their own operating system, they get resources from the host operating system. They are also easily portable as they contain all the libraries and the dependencies to run the application.
What is Docker?¶
Docker is a containerization platform that allows you to package code and dependencies into a Docker image that can be run on any machine. It allows your application to be separated from your infrastructure. The image that you created is portable, so you can run it on any machine that has Docker installed.
Quick Links¶
Getting Started with Pre-Built Docker Images¶
Learn how to quickly start using Bilayers with our pre-built Docker images. Start Here
Creating Interfaces for Your Custom Algorithm¶
Follow our guide to create a web or Jupyter Notebook interface for your deep-learning algorithm. Learn More
Contribution & Developer Guidelines¶
Want to contribute to Bilayers? Check out our developer guidelines and learn how to submit your custom interfaces. Read the Guidelines