CellOrganizer for Singularity¶

About CellOrganizer for Singularity¶

Singularity enables users to have full control of their environment. Singularity containers can be used to package entire scientific workflows, software and libraries, and even data.

CellOrganizer for Singularity is an image with compiled binaries from 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.

Installing CellOrganizer for Singularity¶

About Singularity¶

Singularity performs operating-system-level virtualization. To learn about Singularity and how to use it, click here

Setup¶

The following instructions describe

How to install Singularity, the virtualization engine that will run the container
How to download the latest Cellorganizer image
How to start a shell container from the Singularity image
How to run some of the demos included in the container

Source Code¶

The source code to build the Singularity image can be found at here.

For convenience, the Singularity image can be found at CellOrganizer.

Installing Singularity¶

Before downloading the image, you need to install Singularity. Installing Singularity is beyond the scope of this document.

To follow the official instructions to install Singularity, click here.

Download the repository and build the image using Singularity

Open terminal and enter the commands:

git clone https://github.com/icaoberg/singularity-cellorganizer
cd singularity-cellorganizer
bash ./script.sh .

Download the most recent image using Singularity command line (Recommended)¶

Open terminal and enter the command:

singularity pull shub://murphygroup/singularity-cellorganizer

Pulling the image from Singularity Hub should produce output similar to

Once the download is complete, you can confirm the image was downloaded by listing the singularity images of the repository:

ls murphygroup-singularity-cellorganizer-master-latest.simg

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
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 Singularity¶

List all applications in the cellorganizer-singularity image¶

To list the CellOrganizer functions included in the image, open Terminal and enter the command:

singularity apps  singularity-cellorganizer/murphygroup-singularity-cellorganizer-master-latest.simg

This will display these functions

img2slml
slml2img
slml2info
slml2report
slml2slml

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 this demo, change your current directory to ~/singularity-cellorganizer/demos/2D/demo2D01 by entering:

cd demos/2D/demo2D01

You should find the shell script demo2D01.sh. To run the demo enter the command:

singularity run -a img2slml ../../../murphygroup-singularity-cellorganizer-master-latest.simg demo2D01.sh

The ‘-a’ flag allows us to specify the function binary that we will use in the script. This demo will save a folder param containing .mat files as well as a .mat file lamp2.mat to the same directory (~/singularity-cellorganizer/demos/2D/demo2D01). These .mat files contain information characterizing the trained generative model.

Running the demo in the container should produce results similar to

Run a demo that invokes slml2img¶

An example of a demo that produces simulated images from a trained generative model is demo2D02. To run this demo, change your current directory to /home/singularity-cellorganizer/demos/2D/demo2D02 by entering from your home directory:

cd demos/2D/demo2D02

You should find the shell script demo2D02.sh. To run the demo, enter the command:

singularity run -a slml2img ../../../murphygroup-singularity-cellorganizer-master-latest.simg demo2D02.sh

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

Run custom script that invokes img2slml¶

An example running custom function parameters for img2slml stored within a .txt file. Within this directory (i.e. /path/to/input.txt), you can run the command:

singularity run -a img2slml ~/singularity-cellorganizer/murphygroup-singularity-cellorganizer-master-latest.simg img2slml input.txt