File > Import > Volume Data as Biovels
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Sometimes the original data is too big, or the spacing in the original data is not reasonable, you can modify the Bioxel Size and Original Spacing to adjust the Shape of the Bixoels.
A bioxel is like a pixel, the larger the Bioxel Size, the lower the resolution of the image, Original Spacing will be read from the original data record, but sometimes the image doesn't have original spacing, you may need to input it manually to get the correct shape.
In some cases the environment value is higher than the value of the target object, you can check Invert Scalar to adjust the value for better result.
Many AI segmentation task datasets, provide segmentation data, which are often an integer value representing a layer of segmentation labels. You can set the Label Index to determine exactly which labels to load.
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In 3D view, select bioxels and right-click, Bioxels > Bioxels To Mesh
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File > Export > Biovels as VDB
diff --git a/0.1.x/getting-started/index.html b/0.1.x/getting-started/index.html index 4e3788d..dc6c9b3 100755 --- a/0.1.x/getting-started/index.html +++ b/0.1.x/getting-started/index.html @@ -430,18 +430,27 @@Currently only support Blender 4.0 or above, make sure you have the correct version of Blender.
-Download the latest version https://github.com/OmooLab/BioxelNodes/releases/latest
-In Blender, Edit - Preferences - Add-ons - Install, select the BioxelNodes_{version}.zip you just downloaded.
The add-on requires a third-party python dependency called SimpleITK, click the Install SimpleITK button below to install the dependency. After clicking, blender may get stuck, it is downloading and installing, just wait for a moment. After the Installation, restart blender once.
+In Blender, Edit > Preferences > Add-ons > Install, select theBioxelNodes_{version}.zip you just downloaded.
+The add-on requires a third-party python dependency called SimpleITK, click Install SimpleITK button below to install the dependency. After clicking, blender may get stuck, it is downloading and installing, just wait for a moment. After that, click Reboot Blender button.
This step may have failed due to network factors, just click "Set PyPI Mirror" to change the mirror.
-First you need to have your volumetric data ready. If not, you can access open research data from Dryad (Dryad publishes data exclusively under a Creative Commons Public Domain License)
-Note: Make sure one folder contains only one sequence, multiple sequences need to be manually split into different folders first.
-In Blender, File - Import - Volume Data as Bioxels, select one of the .dcm files and click on "Volume Data as Bioxels" (you can also drag one of the .dcm files directly into the 3D viewport to trigger the import, but this is limited to .dcm format files)
First you need to have your volumetric data ready. If not, you can access open research data from list below：
+| Source | +Object | +
|---|---|
| Dryad | +Open Research Data | +
| OpenOrganelle | +Cells | +
| Embodi3D | +Medical Images | +
| Github | +Medical Images | +
| NIHR | +Medical Images | +
| Medical Segmentation Decathlon | +Medical Images | +
| Allen Cell Explorer | +Cells | +
| Visible Human Project | +Medical Images | +
File > Import > Volume Data as Bioxels, select one of the .dcm files and click on "Volume Data as Bioxels" (you can also drag one of the .dcm files directly into the 3D viewport to trigger the import)
It may take a while to read data. After finishing reading, it will pop up a dialog box
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Ignore the options, just click OK!
-After importing, the necessary nodes are automatically added, the reconstruction and shader are created, and then turned on the cycles rendering to directly see the result.
+After importing, the necessary nodes are automatically added, the reconstruction and shader are created. Click select Bioxels Object, and open the Geometry Nodes panel, change the "Threshold" in segment node.
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and then turned on the cycles rendering to directly see the result.
Click select Bioxels Object, and open the Geometry Nodes panel to see the following node graph:
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You can change the "Threshold" to modify the reconstruction model, or change the "Color", "Density" to modify the shader effect. All the parameters are straightforward, you can understand them by changing the values.
-The node, that named "Segment", is a preset node that combines the steps of 3D reconstruction process and shading process. In general, you need to add one of the segmentation node to reconstruction first, and followed by one of the shader node to set the shader. As you can see in the following figure:
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Currently there are 3 types of nodes
-For example:
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You can add a "Bake" node between segmentation node and shader node, if the reconstruction process consumes too much computing time. But be sure, you are selecting the volume object, not the container object.
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The VDB cache and the Bioxel nodes are not reachable to computers if you don't save them. If you need to give your blender file to someone else, you will need to perform the following steps:
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After that, both the VDB cache and the Bioxel nodes are stored in relative locations. When you share a file with someone, pack the entire directory so that the resources are not lost. The other person will be able to load correctly, regardless of whether they have BioxelNodes installed.
@@ -677,13 +733,13 @@ In Blender,Edit - Preferences - Add-ons - Install, select the The node, that named "Segment", is a preset node that combines the steps of 3D reconstruction process and shading process. In general, you need to add one of the segmentation node to reconstruction first, and followed by one of the shader node to set the shader. As you can see in the following figure:
+
Currently there are 3 types of nodes
+For example:
+
You can add a "Bake" node between segmentation node and shader node, if the reconstruction process consumes too much computing time. But be sure, you are selecting the volume object, not the container object.
+