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5 Tips to Save Time with DICOM Segmentation in Simpleware Software

Posted on 16 September 2024 by Simpleware Support Team
 

DICOM segmentation can be very time-consuming and act as a bottleneck in developing workflows for medical research, device design, pre-surgical planning, 3D printing, and in silico clinical trials. Typically, these processes begin by acquiring DICOM images of anatomical regions using modalities such as Computed Tomography (CT) or Magnetic Resonance Imaging (MRI). DICOM is a complex file format that handles images and data, with each DICOM study having multiple series from an acquisition.

草榴社区 Simpleware software supports the import of various DICOM files and adheres to the DICOM Standard to ensure secure data transfer from sources such as PACS. When working with DICOM data in Simpleware software, the most important information needed for accurately reconstructing volume images is extracted from a directory containing the DICOMDIR files (a summary of what the DICOM contains) and/or the DICOM tags. Simpleware software automatically detects if the selected files are valid and extracts the necessary series (single image volume) information.

Once DICOM data has been imported, it can be segmented to identify regions of interest using different image processing tools. To save time without sacrificing patient data compliance or accuracy, Simpleware software offers several options to streamline the transition from DICOM data to a segmented model, depending on the extent of DICOM segmentation required for a particular workflow. Here we have put together some tips for working with DICOM files:

1) Ensure Patient Data Confidentiality

Working with DICOM series usually involves processing patient image data, which is subject to confidentiality regulations such as GDPR and HIPAA. Personally identifiable data is stored in the DICOM tags and often needs to be anonymized before any segmentation can be carried out. By default, Simpleware software anonymizes DICOM tags as part of the import process. However, it also provides options to anonymize only selected DICOM tags if some imaging data needs to be retained for the workflow

Anonymization options for DICOM tags in Simpleware software

Anonymization options for DICOM tags in Simpleware software.

2) Use Quick and Interactive Tools for Different Tasks

Simpleware software provides quick and interactive tools for working with medical scans to extract regions of interest. The image volume greyscale data (e.g. from CT or MRI) is segmented to create one or more volumes called masks, which are then used to identify particular regions within the background image.

The most common options for obtaining a rapid segmentation include applying a Threshold tool to select a range of greyscales that contain the regions of interest, such as the heart or bone. Following this step with a Mask Flood Fill removes any disconnected regions, while Split Regions enables additional areas that are connected to be removed or separated. For more advanced segmentation where fine details are needed, 3D Editing and manual Painting tools are available.

Simpleware Mask flood fill to acquire regions of interest

Mask flood fill applied to acquire regions of interest.

These off-the-shelf options also work well for low-quality and poor-contrast DICOM data, such as CT scans of muscles or low-contrast MRI data. In this context, tools like the Interpolation Toolbox combine 3D painting of scan data with quick interpolation of the results to obtain the muscle profile. For MRI data, a selection of slices can be painted before using a 3D Wrap filter to generate a mask without the need to paint on every single slice of the image data.

3) Take Advantage of the GUI and Scripting

Everyday use of the software involving large amounts of DICOM import and segmentation can be made more straightforward by collecting commonly used segmentation tools in the My Tools ribbon. Scripting options in the Simpleware Scripting API are available to speed up common workflows using Python and C#. Less experienced users can also record steps with a Macro option, while those who want to add their own filters or tools can import them as Plug-Ins. Running the software from the Command Line similarly makes it easier to create a workflow with other programs that involve repeatable segmentation steps. More experienced Simpleware software users have many options to customize the GUI with small scripts, which work particularly well when processing a large number of similar datasets.

The Simpleware scripting interface

The Simpleware interface showing the Scripting tab; (A) shows the Macro record option, (B) shows the option to convert from the Log tab to a script.

4) Automate DICOM Segmentation

The Simpleware AI-based machine learning algorithms are making it easier to significantly speed up common DICOM segmentation workflows for a variety of anatomies such as hips, knees, and hearts. Trained algorithms can automatically segment and add landmarks to DICOM data, reducing the amount of manual intervention needed by users, who then only need to review and make any remaining edits. The key advantage of this approach to DICOM segmentation is that it frees up time for users during the initial image processing stage, allowing them to move faster to the next phases of the workflow, such as design, 3D printing, and simulation.

The Simpleware Hip Revision CT tool

The AI-powered Simpleware Hip Revision CT tool.

5) Scale Up Automation

It is becoming increasingly important for those segmenting DICOM data to scale up their workflows to account for large studies. For example, processing hundreds of scans per month for surgical planning or in silico modeling requires a lot of datasets to be processed. For these situations, the Simpleware team provides fully customized single-check solutions using AI/ML techniques for specific series of steps and requirements. With this approach, common DICOM segmentation tasks can be integrated into a repeatable workflow able to scale to hundreds or thousands of cases every month, enabling patient-specific designs and other decisions to be made without undue delay.

The Simpleware spectrum of automation

DICOM segmentation can be scaled up to thousands of cases.

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Any Questions?

If you would like to know more, please contact us. Our technical specialists will be happy to help you with any questions or challenges you are facing.