CellOrganizer for Docker

CellOrganizer for Docker contains binaries for the functions

• img2slml, the top-level function to train generative models of cell morphology, and
• slml2img, the top-level function to generate simulated instances from a trained generative model,
• slml2info, the top-level function to generate a report from information extracted from a single generative model.
• slml2report, the top-level function to generate a report from comparing generative models.
• slml2slml, the top-level function to combine models into a single model file.

Downloads

Instructions on installing Docker and downloading the CellOrganizer for Docker image can be found below

Additional Files

The image contains the following libraries, models and images.

• CellOrganizer for Matlab binaries
• Generative models
• Murphy Lab 2D/3D HeLa datasets
• BioFormats tools

Important terms

Docker

an open-source project that automates the deployment of software applications inside containers by providing an additional layer of abstraction and automation of OS-level virtualization on Linux.

What are containers?

The industry standard today is to use Virtual Machines (VMs) to run software applications. VMs run applications inside a guest Operating System, which runs on virtual hardware powered by the server’s host OS.

VMs are great at providing full process isolation for applications: there are very few ways a problem in the host operating system can affect the software running in the guest operating system, and vice-versa. But this isolation comes at great cost — the computational overhead spent virtualizing hardware for a guest OS to use is substantial.

Containers take a different approach: by leveraging the low-level mechanics of the host operating system, containers provide most of the isolation of virtual machines at a fraction of the computing power.

• Images – The blueprints of our application which form the basis of containers. 

• Containers – Created from Docker images and run the actual application. A list of running containers can be seen using the docker ps command.

• Docker Daemon – The background service running on the host that manages building, running and distributing Docker containers. The daemon is the process that runs in the operating system which clients talk to.

• Docker Client – The command line tool that allows the user to interact with the daemon. More generally, there can be other forms of clients too – such as Kitematic which provide a GUI to the users.

• Docker Hub – A registry of Docker images. You can think of the registry as a directory of all available Docker images. If required, one can host their own Docker registries and can use them for pulling images.

[ taken from: https://docs.docker.com/get-started/overview/]