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

• Conda

• Jupyter

• and the Python packages

  • cellorganizer-python 2.9.0

  • ipywidgets 7.4

  • pandas 0.24

  • numexpr 2.6

  • matplotlib 3.0

  • scipy 1.2

  • seaborn 0.9

  • scikit-learn 0.20

  • scikit-image 0.14

  • sympy 1.3

  • cython 0.29

  • patsy 0.5

  • statsmodels 0.9

  • cloudpickle 0.8

  • dill 0.2

  • dask 1.1

  • numba 0.42

  • bokeh 1.0

  • sqlalchemy 1.3

  • hdf5 1.10

  • h5py 2.9

  • vincent 0.4

  • beautifulsoup4 4.7

  • protobuf 3.7

  • xlrd

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

Setup

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 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

Searching for CellOrganizer should return a container like the image below

Then click CREATE to download the image and start a container

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			v2.8.1
demo2D04	True
demo2D05	True
demo2D06		True
demo2D07		True
demo2D08	True
demo2D09	True
demo3D00		True
demo3D01		True
demo3D04		True
demo3D05		True
demo3D06		True		v2.8.1
demo3D07		True
demo3D08		True
demo3D09		True
demo3D10		True
demo3D12	True
demo3D19	True		Report
demo3D25		True
demo3D47			Model
demo3D48	True
demo3D50	True
demo3D51	True		Plot
demo3D52	True
demo3D53		True
demo3D55		True	Plot
demo3D57		True	Plot
demo3D58		True
demo3D59		True

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.

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.

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.

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.

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.

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