We worked with the team at Instructables to create 3D prints of a muscle in the horse that is important in locomotion. The deep digital flexor muscle and tendon unit acts like a spring--it stores large amounts of energy so that horses can gallop at high speeds in an energetically efficient manner. Like our horse bone 3D print, our goal was to visualize internal structures--in this case, the tendons within the muscle. We first obtained an MRI scan of a horse’s hindlimb (see region labeled in photograph), then created 3D models for the muscle and tendon from the images. We used the the Instructables’ 3D printer to print a two-material model, with the muscle printed in a clear resin and the tendon printed in opaque white material.
Step 1: Materials and tools
ImageJ or other image segmentation software that can import medical images
Meshlab - surface model editor
There are a number of options for image segmentation and model editing software, some with quite sophisticated algorithms that might be needed for challenging image sets. We describe the open source options in this Instructable (ImageJ, Meshlab, Blender), though some processes may be done more easily with proprietary software packages (e.g. Mimicis, Simpleware).
Step 2: Get an MRI scan of a muscle
Step 3: Segment the region of interest from the scan
(Alternatively, there are software packages that specialize in segmentation and model creation from medical images such as MRI and CT scans that are costly but are useful for this step, e.g. Mimics, Simpleware, Amira. 3D slicer is a free alternative to ImageJ.)
This was done manually on each of the 196 slices by painting our desired region using the selection brush. Our region is surrounded by similar looking muscle, and in some slices they blend together, so there was not an easy, automated method of identifying our region. This process would not be efficient or practical if we had to segment many MRI scans, but for a single scan it was a reasonable method. In the image above, the red region identifies the region that we want to model.
Step 4: Isolate the segmented region for further segmentation
Step 5: Segment the tendon region within the ROI
Note that the ease of segmentation is highly dependent on the quality of the image scan! For example, an artifact such as a background gradient may require more sophisticated segmentation algorithms than basic thresholding.
Step 6: Create surfaces from segmentations
Once we had the whole muscle-tendon STL and the tendon STL, we used Meshlab to clean and smooth the surface models. The tendon model is jagged-looking when first exported because of the voxels in the original MRI scan; the smoothing algorithm gets rid of the rough appearance and also eliminates small islands of the model that are not connected to the main Then we used Blender to subtract the tendon model from the whole muscle-tendon model using a boolean modifier. Finally we have a model for the muscle region excluding the tendon--this surface model was export as an STL.
We were interested in visualizing how the branches of the tendons were oriented within the muscle, so we divided the model further by creating sections--this was also done using boolean operations within Blender.