HOW TO SEGMENT OUT AN INDIVIDUAL FISH FROM A SCAN OF MULTIPLE SPECIMENS USING 3D SLICER

- Christian Graca, Shrusti Brahmbhatt, and Windsor Aguirre

BASIC INFORMATION• 3D Slicer Version: 4.11• Written by: Christian Graca, Shrusti Brahmbhatt, and Windsor Aguirre• Date Created: July 6, 2021• Last Updated: July 21, 2021• Original Source: Modified from https://youtu.be/GgPRsQYkGbc

INTRODUCTION• Micro-CT scanning is time consuming so

researchers will often scan multiple individuals together in a single scan and then separate them for individual analysis using a program.

• In this tutorial, we cover how to isolate an individual fish skeleton from a scan of multiple fish skeletons, e.g., a “fish burrito”, in 3D Slicer.

• This tutorial begins after a scene has been created showing the fish skeletons using the volume rendering function. See the Getting Started module above this tutorial.

STEP 1:VOLUME RENDERING

Go to the Volume Rendering module (under Modules). Check Enable under Crop in the left window and click on the eyeball icon next to Display ROI in order to display the ROI (Region of Interest) and adjust it in order to focus on the region of interest.

STEP 1:VOLUME RENDERING

• The ROI should be focused on one fish. To do this, you can adjust the individual 2D views using the red (anterior to posterior), green (ventral to dorsal) and yellow (from left to rights) bars (indicated by the arrows) so that complete skeletons are visible (modify the bars so they are all completely to the left or right).

HOW TO ADJUST THE ROI (REGION OF INTEREST)?Once you have used the red, yellow, and green bars to adjust the screen in order to see all the skeletons clearly, clicking on display ROI will display a white box around the specimens which will have red, purple, green, yellow, and orange circles which you can adjust to focus on one fish by using the mouse.

STEP 2: CONVERTERS MODULESwitch to the Converters module under modules. Select the Crop volume submodule.

STEP 2: CONVERTERS MODULE

Select the input volume, the volume that you would like to crop (we named ours 1Unnamed series) and for Input ROI select Annotation ROI. For the Output volumeselect create new volume as (we renamed it Segmentation1). Then click Apply.

STEP 3: DATA MODULE

Switch to the Data module under Modules.Click on the eye icon next to Segmentation1

STEP 3: DATA MODULE

• Clicking on the eye icon next to Segmentation1 will give you the desired result- a fish isolated from a scan of multiple fishes.

STEP 4: VOLUME RENDERING MODULE

Go back to the Volume Rendering module in order to get rid of the original volume that is being rendered. Turn on the volume rendering for the new volume (which in this case is Segmentation1). Select the Preset as CT-Bone; Rendering- VTK CPU Ray Casting; Under Techniques select Maximum Intensity Projection. Use the Shift Slider to get a clear image.

STEP 4: VOLUME RENDERING MODULE

The final image of the isolated fish will look like the picture on the left.

STEP 5: SAVING THE SCENE

• Click on the SAVE box on the top left corner of the screen in order to save the segmented fish scene.• Select all the file names (as shown in the picture on right) and click SAVE in order to save the scene on your computer.