Creating and Exporting Isosurfaces

How to go from a volumetric image to a mesh, and exporting it as STL.

1. Hi there

After opening sciview, you are presented with the main window. In case the inspector on the right is not shown, you can double-click the tool icon in the tab bar to toggle it.

2. Open your file

Open your file of interest from the Fiji main window. In this example, we use the T1 Head (16-bits)example image provided with Fiji.

3. Figure out the isosurface value

When hovering with the mouse over the image you've just opened, Fiji will tell you the greyscale value under the cursor in the main window. you can use this to figure out the value you would like to use for the isosurface. In this example, we use 399.

4. Create the isosurface

In the sciview window, click Process > Isosurface. This will open the window above. Enter the isosurface value you have determined. In case you have multiple images open in Fiji, these will show up in the Image dropdown. Be sure to select the correct image. Then click OK to create the isosurface. This might take a little while, depending on the size of the dataset.
Note: Due to an issue with Fiji, an error might be displayed when opening the Isosurface tool. You can safely ignore this and close the console window.

5. Inspect the Isosurface

After sciview is done with processing, the isosurface will show up as Mesh in the sciview inspector on the right. You can double-click the Mesh object and then use Shift-MouseDrag in the main window to rotate around the mesh. If you are satisfied with the result, proceed to the next step. If not, you can delete the isosurface by right-clicking on Mesh, and selecting Delete.

6. Exporting as STL

To finally export the isosurface as STL file, simply select File > Export as STL in the sciview main window.