StrainMap

Copyright (c) 2022, Imperial College London All rights reserved.

StrainMap provides a user-friendly and efficient way to analyse MRI data acquired with a novel, high temporal and spatial resolution velocity-encoded MRI technique suitable for regional strain analysis in a short breath-hold. These images include magnitude and phase components.

The segmentation stage lets the user select the inner and outer walls of the heart. This needs to be done for all images taken over a heartbeat and for as many slices (cross-sections of the heart) as available. The process can be manual – very long – or assisted by several machine learning technologies such as snakes segmentation or a deep neural network. The segmented heart, together with the phase information can be used in the next stage to extract information of the instantaneous, spatially-resolved velocity of the myocardium during the heartbeat in the form of velocity curves ad heatmaps. All this information can be exported for further analysis elsewhere.

Installation

Recommended way

The recommended way for end users to access and use the tool is via pipx:

1. Install and configure pipx following the instructions appropriate for your operative system. Make sure it works well before moving on.
2. Install StrainMap with pipx install strainmap. It might take a while to complete, but afterwards updates should be pretty fast.
3. To run StrainMap just open a terminal and execute strainmap. You might want to create a shortcut for this command in the desktop, for convenience.

Whenever there is a new version of StrainMap, just run pipx upgrade strainmap and it will be downloaded and installed with no fuss.

Use a StrainMap executable

Alternatively, you can download from the release page the self-contained executable corresponding to the version you are interested in. Bear in mind that these executables contain StrainMap and all its dependencies, meaning that each download can be, potentially, very large.

For developers

This installation instructions assume the following pre-requisites:

• Python >=3.8
• Poetry >= 1.11
• Git

If these are already installed and the path correctly configured, the following should download the last version of StrainMap, create and activate a virtual environment, install all StrainMap dependencies and, finally, install StrainMap itself in development mode.

git clone https://github.com/ImperialCollegeLondon/strainmap.git
cd strainmap
poetry install

To use StrainMap simply run:

poetry run python -m strainmap

Related projects

The following two projects are standalone tools used to collect the data needed to train the AI used by StrainMap and re-train it, when needed. They are separate from StrainMap and are not required for using it.

• AI Trainer
• Files Harvester