CellOrganizer for Docker

About CellOrganizer for Docker

CellOrganizer for Docker is an image with compiled binaries from the CellOrganizer functions

  • img2slml, the top-level function to train generative models of cells, 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.

The image also comes with

About Docker

Docker performs operating-system-level virtualization. Docker lets us create and deploy a preconfigured image with the CellOrganizer binaries. This image can be used to spin containers that are ready to use and start testing.

To learn about Docker and how to use it, click here

About Jupyter

The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text.

To learn more about Jupyter, click here

Installing CellOrganizer for Docker

The instructions below describe

  • How to install Docker, the virtualization engine that will run the container

  • How to install Kitematic, a UI for Docker

  • How to download the latest cellorganizer-docker image from Docker Hub, i.e. the docker images repository

  • How to start a container from the Docker image

  • How to connect to the container

  • How to run some of the demos included in the container

Installing Docker

Before downloading the image and spinning a container, you need to install Docker. Installing Docker is beyond the scope of this document. To learn about Docker Community Edition (CE), click here.

  • To install Docker-for-Mac, click here.

  • To install Docker-for-Windows, click here.

Installing Kitematic and downloading CellOrganizer for Docker

The easiest way to download an image and run a container is to use Kitematic. Kitematic is a tool for downloading images and running containers.

  • To install Kitematic, click here.

Attention

Kitematic is not necessary, but it is recommended to streamline installation and deployment.

Download the most recent image using Kitematic

Start Kitematic. It should open a window similar to the screenshot below

../_images/kitematic.png

Searching for CellOrganizer should return a container like the image below

chapters/image_find.png

Then click CREATE to download the image and start a container

chapters/Image_Downloading.png

Download the most recent image from terminal

For convenience, the Docker image can be found in Docker Hub along with links to the Dockerfile.

Demos

There are several demos included within the CellOrganizer software bundle. These demos are intended to illustrate CellOrganizer’s functionality, and should be used to familiarize the user with the input/output format of various top-level functions such as img2slml and slml2img. Certains demos have been deprecated and will be removed in future versions of CellOrganizer.

Demo

Training

Synthesis

Other

Deprecated

demo2D00

True

demo2D01

True

demo2D02

True

demo2D03

True

X

demo2D04

True

demo2D05

True

demo2D06

True

demo2D07

True

demo2D08

True

demo2D09

True

demo3D00

True

demo3D01

True

demo3D04

True

demo3D05

True

demo3D06

True

X

demo3D07

True

demo3D08

True

demo3D09

True

demo3D10

True

demo3D11

True

demo3D12

True

demo3D15

True

demo3D17

True

demo3D19

(True)

Report

demo3D20

(True)

Plot

demo3D25

True

demo3D29

(True)

Info

demo3D34

True

demo3D35

(True)

Info

demo3D42

True

demo3D44

True

demo3D47

Model

demo3D48

True

demo3D50

True

demo3D51

(True)

Plot

demo3D52

True

demo3D53

True

demo3D55

(True)

Plot

Running CellOrganizer for Docker through Jupyter-Notebook

After the docker image has been created through Kitematic, click the top right button to open the Jupyter server.

chapters/Web_Click.png

This will open a webpage on your browser that is hosted by your local machine. The environment will intially contain Ipython notebooks with preinstalled demos that will run the CellOrganizer binaries.

chapters/home_page.png

Run a demo that invokes img2slml

An example of a demo that trains a generative model from a series of .tif image files is demo2D01. To run a demo, simply click the run button at the top of the notebook.

chapters/Run_Button.png

This demo will save a folder param containing .mat files as well as a .mat file lamp2.mat to the same directory (/home/cellorganizer/demos/2D/demo2D01). These .mat files contain information characterizing the trained generative model.

Run a demo that invokes slml2img

An example of a demo that produces simulated images from a trained generative model is demo2D02.

This demo will save a folder img containing these simulated images to the same directory.

Export generated data out of the container

To export generated data out of the container, click the files in the directory that will be exported and click download.

chapters/Download.png