Image Data Segmentation

Segmentation is the process of converting 2-dimensional DICOM files into a 3-dimensional volume, usually for placing anatomy into VR/AR or producing a 3D print. Objects are typically created for educational purposes, explaining a procedure to patients and pre-surgical planning. There are a number of software packages that assist in this transformation, however the Earl E. Bakken Medical Devices Center (Bakken MDC) primarily uses Mimics by Materialise.

The Bakken MDC is HIPAA compliant and uses BOX to receive files from radiologists. We can also receive files by dropping off a CD with our staff. All CD’s are stored under triple lock-and-key.

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  1. What makes a good DICOM?
    • We prefer slices of <1mm, a 10% - 30% slice gap and isotropic voxels. If possible, the use of ‘contrast’ helps to distinguish between the tissues.
  2. Can I order multiple models at once?
    • Yes, multiple models may be ordered at once. If two different structures are desired from the same DICOM file, upload the one DICOM file and mention in the Description and the Comments which anatomical features should be segmented.
  3. What kind of anatomy is acceptable to be segmented?
    • Our team has worked with dense tissue, such as bone, all the way to softer tissues, such as hearts and brains.
  4. What is a “model for scheduled surgery,” as listed on the order form?
    • The Bakken MDC works closely with medical professionals. In part of that relationship, we make models of patient anatomy for the doctor to analyze – and even practice on – prior to performing surgery on said patient.
  5. When can I expect my model to be finished?
    • You’ll receive a confirmation that we’ve received your model, a project timeline and cost estimate within 1-3 business days.

Submission Form

First and Last Name:
Email Address:
Phone Number:
Affiliation (Company or UofMN Department)
Principal Investigator (PI)
EFS String (for UMN Projects ONLY)
Description of Work to be completed (ex: right ventricle model)
Is this for Pre-Surgical Planning
When do you need the work done?
I will be viewing the results as a VR/AR Model
3D Print

*We will contact you about the transfer of the DICOM files after we review the order form.

Celiac Model

For more information
[email protected]