3. Objects

Microscopy Nodes loads your microscopy data as different types of objects, depending on how you loaded each channel.

mic nodes objects

Each type of object is placed in a holder collection. The Axes and Slice Cube are always present.

You can select an object by clicking on it in the outliner (as shown in the screenshot) and change its properties:

Change underlying data in the modifier menu of the properties or the (advanced) Geometry Nodes workspace
Change visualization in the material menu of the properties or the Shader Nodes workspace

The exact settings and where to change them change per object, so see below.

Holder

The Holder is an empty object which is the parent of the other Microscopy Nodes objects.

The holder can be scaled, moved and rotated and then all of its objects will be transformed along with it.

Axes

The Axes object is always loaded with your dataset. It draws a scale grid based on the number of pixels, pixel size, and pixel unit.

Geometry options
- pixel unit per tick
  
  The distance between grid lines
- Grid
  
  Whether to draw a grid or only a box
- Line thickness
  
  Thickness of lines in arbitrary units
- Frontface culling
  
  If ticked, clips out the axes that are closest to the camera or viewpoint, so that they do not obstruct the view.
- Separate planes
  
  For each plane (xy bottom, top etc) you can select whether they will be drawn
Shader options
- Color

Scale grids can be moved, scaled and rotated independently of the holder without losing their accuracy.

Bars versus grids

In Microscopy Nodes, only scale grids are shown. Blender’s default cameras are perspective cameras, where traditional scale bars are not very meaningful. We'll probably add support for some form of scale bar in the future for orthographic renders.

Volumes

The Volume holds channels of volumetric data, which can be rendered either as emitting or scattering light. It is generated when you enable Volume during loading.

Geometry options
- Included channels
  
  If channels are not included, they are also not loaded into RAM
Shader options
- Pixel intensities
- Opacity calculation
- Color LUT

The easiest way to edit a volume shader is in the Shader Nodes workspace, where you can most easily switch between channels in the properties.

You can toggle between emission and scattering modes using the emission toggle in loading.

Surfaces

The Surface object is a mesh extracted from a volume using an isosurface threshold. It is generated when you enable Surface during loading.

Geometry options
- Included channels
- Threshold
  
  The intensity value above which the surface is extracted.
- Voxel size (only listed if Mesh Resolution is not Actual)
  
  Interactive scalable unit for mesh detail
Shader options
- Standard mesh shading parameters (color, opacity etc)

Label Masks

The Label Mask object is a mesh generated from a label image, such as a segmentation channel. It is generated when you enable Labelmask during loading.

Each value in the volume is turned into a separate mesh.

Geometry options
- Included channels
Shader options
- Color per label
- Revolving colormap or linearly distributed among objects
- Standard mesh shading parameters (color, opacity etc)

Slice Cube

The Slice Cube is a movable object that defines the visibility of other objects.

The slice cube is inherently nothing else than a Cube with a transparent shader. The linkage to its transparency is done from the shader of the sliced object. This means you can also add a new cube and point to this instead.

This has no Geometry options or Shader options

How the Microcopy Nodes objects work

The data objects are Geometry Nodes objects that reference preloaded data stored in the cache collection. In the Geometry Nodes workspace you can add edit the loaded data and add modifiers.