Top Tips to Speed up Cardiovascular Image Segmentation

Posted on 7 July 2020 by Celia Butler

Segmenting the Cardiovascular system can be very time consuming. The quality of the data varies widely with the part of the body that is being imaged – the heart being one of the most complex. Models created from this type of image data are often using for planning, 3D printing, or CFD or FE analysis.

Simpleware ScanIP offers a medical image segmentation solution to generate robust models that do not need any “fixing”. Here we have put together top tips for working with cardiovascular data to obtain accurate and robust 3D models.

1. Use Automated Tools to Segment Image Data

Simpleware recently released a new module, Simpleware AS Cardio, designed to take all the hassle out of segmenting hearts from CT data. This one-click solution allows you to segment the heart and create key landmarks in a couple of minutes (or faster) instead of hours. This tool is a time and effort saver for those working with a few to thousands of datasets.

The tools are currently available when working on images from CT to extract right and left atriums and ventricles, aorta, pulmonary artery, and myocardium. Landmarks are placed in key positions on the aorta and left ventricle.

Simpleware AS Cardio heart segmentation tool and output

Simpleware AS Cardio heart segmentation tool and output.

Not working with hearts? Contact Us to see what we can do for you.

2. Combine Specialist Tools to Avoid Manual Segmentation

Manual segmentation can be very time-consuming when working with complex data in 2D or 3D. Simpleware software has a full suite of medical image segmentation tools which have been developed with our customers to quickly generate good quality models.

Using a combination of these tools allows you to generate at least the basis for a good model. For example, considering heart CT, we can use the Threshold tool to select a range of greyscales that include the sections of the heart required, followed by a Mask Flood Fill to remove any disconnected regions. If there are still areas which are connected which need to be removed or just separated in another mask, the Split Regions tool can be used.

Split tool in Simpleware ScanIP for separating connected regions of the image data

Use the Split tool in Simpleware ScanIP for separating connected regions of the image data.

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3. Tidy Up Segmentation with the Help of some Quick Tool

After using tools like Threshold or Region Growing, you may be left with some tidying up to do. This can be sped up using a range of tools from the Image Processing tab. Use Island Removal to get rid of regions smaller than a specified number of voxels, or Fill Gaps to close up cavities inside objects or at the image boundaries.

The Morphological tools are also key for removing thin connections between two blood vessels (using an Open filter), or closing small holes caused by noise or imperfections in the image acquisition process.

Island Removal tool in Simpleware ScanIP to delete small regions

Use the Island Removal tool to delete small regions.

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4. Make the Most of 3D Editing

3D Editing tools can be used to identify a specific area you want to work with and apply a range of filters in just that region. The regions can be selected using a range of techniques, from hand-drawn Lasso Frustums to delete small specific parts, to Spheres to close holes or smooth unrelated features (which may not be relevant for your analysis).

Simpleware ScanIP offers Simple 3D Editing for quick adjustments, such as deleting unrelated regions, as well as Advanced 3D Editing for selecting and adjusting more precise or complex regions.

Advanced 3D editing tools in Simpleware ScanIP

Advanced 3D editing tools in Simpleware ScanIP offer intuitive ways to segment data.

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5. Use Intuitive Tools to Solve Problems Caused by Low Contrast or Artefacts

CT data presents challenges for segmenting muscles and vessels using threshold tools due to low contrast results. To reduce time-consuming manual segmentation, the Interpolation Toolbox in Simpleware software allows you to combine 3D painting of scan data with a quick interpolation of the results to obtain the profile of the muscle or vessel.

Similarly, with MRI data that is low-contrast, you can paint on a selection of slices in each view - a 3D Wrap filter then creates a mask, removing the need to paint on every single slice of the image data.

Propagation and interpolation tools in Simpleware software

Propagation and interpolation tools in Simpleware software.

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6. Strengthen your Models for CFD Simulation

When considering the flow in blood vessels, it can be useful to set a minimum diameter and combine this with your geometry in order to ensure that vessels don’t artificially collapse in simulation. This can be done by Sweeping a circular cross section along the centreline structure of the vessel network, and then combining it with the original segmentation to keep all topological accuracy larger than the minimum diameter.

Sweep centerlines to create a minimum vessel diameter

Sweep centerlines to create a minimum vessel diameter.

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7. Customize and Automate Workflows

Simpleware software can be augmented for specific workflows with small scripts. Scripting and customization options in the software can be useful to cut down on manual work. For example, if you are working with many similar datasets, scripting can often be utilized to automate repetitive tasks and reduce segmentation time. For more information see the Customization blog. For more information on our customization tools, please read our blog Customize and Automate Workflows with Simpleware Software.

Simpleware scripting functionality to automate repetitive tasks

Use the Simpleware scripting functionality to automate repetitive tasks.

Learn More

We hope these tips provide a good introduction to some of the tools available in Simpleware software to quickly segment cardiovascular data. For more details, check out our recorded web workshop on this subject:

Any Questions?

Want to know more about how Simpleware automated solutions can improve your workflows, or have questions about applying these techniques to different anatomies?