MIAAIM: multi-omics image alignment and analysis by information manifolds

MIAAIM is a software to align multiple-omics tissue imaging data. The worflow includes high-dimensional image compression, registration, and transforming images to align in the same spatial domain. MIAAIM was developed at the Vaccine and Immunotherapy Center at MGH in the labs of Dr. Patrick Reeves and Dr. Ruxandra Sîrbulescu. MIAAIM is written in Nextflow with containerized workflows to enable modular development and application across diverse computing architectures.

MIAAIM in Python

If you are not comfortable running Nextflow, or if your pipeline needs to be tailored for a specific application, please feel free to navigate to MIAAIM in Python.

Installation

MIAAIM uses nextflow, which requires Java 8 or later.

Linux / OS X

To get started with MIAAIM:

1. Install Docker. You can ensure that Docker is available to your system using the command docker images
2. Install Nextflow using curl -s https://get.nextflow.io | bash
3. You can check that Nextflow is installed by calling it in the context of the directory that you installed it in with ./nextflow run.
4. (Recommended) If you want to be able to call Nextflow directly from the command line without entering the path to it, enter the follwing command:

 chmod +x nextflow    # be able to call nextflow

Windows

To run Nextflow in Windows, you will need to install WSL prior to installing Nextflow. To do this, follow these steps:

1. Open Windows Powershell as administrator.
2. Download WSL by typing dism.exe /online /enable-feature /featurename:Microsoft-Windows-Subsystem-Linux /all /norestart
3. Enable virtual machine dism.exe /online /enable-feature /featurename:VirtualMachinePlatform /all /norestart
4. Download the latest Linux kernel update package (https://wslstorestorage.blob.core.windows.net/wslblob/wsl_update_x64.msi).
5. Set WSL2 as your default kernel by typing wsl --set-default-version 2
6. Install linux distribution -- we have tested MIAAIM successfully using Ubuntu 20.04 LTS.
7. Open your Ubuntu installation (you will be asked to set up your installation by providing a user name and password)
8. Within the Ubuntu shell enter the following commands to install necessary components for Nextflow and pulling the MIAAIM repository from GitHub:

sudo apt update
sudo apt install openjdk-14-jre-headless
curl -s https://get.nextflow.io | bash
chmod +x nextflow
sudo apt-get -y install git

9. Now install Docker for windows and allow it to connect with your WSL2 (see here for details). You should now be able to run nextflow and MIAAIM within your installed WSL!

Funding

This work is supported by philanthropic funding at the Vaccine and Immunotherapy Center. Joshua Hess is supported by the NSF Graduate Research Fellowship under grant no. 1746886.