During the July 2021 SPARC Codeathon, we devised a way to convert a SPARC Scaffold into a HuBMAP CCF Reference Organ. This will facilitate mapping data from SPARC to HuBMAP (and vice versa). Below is a description of the workflow used to convert the SPARC Human Stomach Scaffold. While we did not have time to do more scaffolds, the workflow here should apply to any scaffold which includes a VTK version of the scaffold.
Before starting, you will need to install:
- Download and install Paraview Desktop. This application supports exporting a VTK files to GLTF.
- Download and install Blender. This application supports modifying and exporting GLTF files to binary GLB format.
- Install your IDE of choice. We recommend Visual Studio Code.
- Create a
humanStomachfolder to place files in for testing/development.
You can find the human stomach scaffold on the sparc.science website (direct download). Download the humanStomach.vtk file into your humanStomach folder.
Open the ParaView Desktop app (directions vary by platform), click File/Open, and select the downloaded humanStomach.vtk file. When loaded, you will initially see a blank scene. Press the eye icon next to humanStomach.vtk in the Pipeline Browser to see the scaffold.
Next switch the Coloring to Solid Color in the Properties tab. Then click Edit below Solid Color and use this HTML Color Code: #EA5162. Depending on the organ, a different color may be chosen.
Now export the humanStomach.vtk to GLTF by clicking File/Export Scene..., switching Files of type: to .GLTF Files (*.gltf) and save as humanStomach.gltf.
You can now close out the Paraview Desktop app.
Open the Blender desktop app (directions vary by platform). When first opened, there is a default scene with a solid cube. Drag to select the cube, camera, and lighting and press the delete key to remove them from the scene.
Next, import the humanStomach.gltf file by clicking File/Import/glTF 2.0 (.glb/.gltf) and selecting the file from the file chooser. The organ may be very large when first opened, so zoom out to get a view of the organ.
Expand the tree in the Scene Collection pane at the top-right. Delete the Camera Node, rename Renderer Node to SPARCF, and rename both mesh0 items to SPARCF_stomach.
Before:
After:
Finally, click File/Export/glTF 2.0 (.glb/.gltf), change the Format to glTF Binary (.glb), expand Geometry and check Tangents (in addition to the default selections), and save the scene to humanStomach_F.glb.
Keep the scene open for the next step: saving the 'male' version.
In the CCF we currently have to have both a Male and Female version of each Reference Organ and they must have unique scene node names. Thus, we use the form xxxF for the top level node and xxxxF_structure for the organs/structures within. Male forms are formatted analygously with xxxM.
In the Scene Collection pane at the top-right rename all SPARCF strings to SPARCM for male. Then save the scene to humanStomach_M.glb using the same steps as was used for the 'female' version.
You may need to come back to Blender to check dimensions, how far to transform things, etc. But at this stage, take note of the dimensions in preparation for the next stage and close out Blender.
Go to the CCF Registration User Interface (RUI) and create two RUI registrations using the tissue dimensions noted above. Place the 'Tissue' relative to the Skin reference organ for both Male and Female. Use the REVIEW AND DOWNLOAD button to save the RUI locations named humanStomach.VHMSkin.rui_location.json and humanStomach.VHFSkin.rui_location.json respectively.
In order for the scaffolds to be recognized as reference organs, some modifications need to be made to have them be recognized and loaded. You can see the results of the modifications here and here.
Modify the ccf-eui.html file to include the reference organ files in the dataSources array.
At time of writing, there are still some issues to be worked out and to better streamline the process. Reach out via Slack or a GitHub Issue if you need assistance.