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1. First Use

Installing Microscopy Nodes

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  1. Open Blender.
  2. Navigate to Edit > Preferences.
  3. In the Add-ons tab, search for Microscopy Nodes.
  4. Click Install to download and enable the add-on.

Blender Interface Overview

The Blender interface is very flexible and can be reconfigured in many ways. While this is a powerful feature, it also means that explaining the basics can be a bit technical, and some of the terms are Blender jargon. To make things easier, here is a quick overview of some key terms and where to find common functions.

Further information and navigation can be found in the Blender Manual

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The Blender interface always contains:

  1. Top bar: contains the main menus and selection of the tabs, or workspaces (e.g. Layout, Shading, Geometry Nodes).
  2. Workspace: Reconfigurable workspace. Contains different areas depending on the selection in the topbar.
  3. Status bar: contains shortcuts suggestions

But it can be configured much more with workspaces . Currently we're in the Layout workspace.

Layout Workspace

The Layout workspace (by default selected in the topbar) is our main workspace, made for assembling and seeing your 3D scene. This contains multiple elements with Blender-specific names:

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  1. 3D Viewport: Main 3D interaction area.
  2. Outliner: Tree view of all objects in the scene. This is the easiest place to select objects.
  3. Properties Editor: Edit properties of the scene and the selected object. Under you can find Microscopy Nodes.
  4. Timeline: For animation.

With Microscopy Nodes, we also use the Shading workspace, and for advanced users, the Geometry Nodes and Scripting workspaces.

The 3D Viewport

Annotated on the right in the image are widgets you can drag to rotate (axes), scale and move the view.

Mouse navigation is possible and configurable in the Preferences. This depends on which input device you use (2-button mouse, 3-button mouse, touchpad).

The View menu

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At the top of the 3D viewport, there is a dropdown menu called View - this has shortcuts and other tools to align the view.

For example, if you lose all the objects in the scene, you can select an object in the outliner in the top right, and use the menu View > Frame Selected (or just View > Frame All) to see your scene again.

The outliner

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The outliner lists all collections and objects in the scene. Here you can select objects more easily.

This also provides an interface for visibility in the / 3D viewport, and in the / final render. If objects are not visible, they are also not loaded into RAM, so it can speed up Blender to limit visibility.

Manipulating Objects

Annotated on the left in the image are widgets you can drag to select, move, rotate and scale objects. The transform widgets spawn a gizmo: a mouse-clickable interaction interface: transform gizmos

Transforms can also be done with hotkeys: G for grab/move, R for rotate, S for scale. The transformation can be locked to an axis with the X, Y orZ key.

Adding an object

At the top of the 3D viewport is an Add menu, from which you can add different primitive objects, such as a camera or lights. This is also findable under the key combination Shift + A

To add microscopy data, there is a separate loading window.

Deleting objects

You can select any object in the viewport or outliner, and delete it by Right Mouse Button > Delete Object or pressing X and confirming.

For deleting all objects in the scene, it is fastest to press A to select all objects and X to delete them.

In the outliner, an entire group can be deleted at once with Right Mouse Button > Delete Hierarchy

Viewport rendering

In the top right of the viewport you can change the way the contents are shown.

Microscopy Nodes volume data will only be visible in Material Preview and Rendered mode.

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From left to right:

  1. Wireframe : Only the object skeleton, No volumetric data shown.
  2. Solid Mode: Only the external surfaces are drawn
  3. Material Preview: Is meant for previewing your scene without full calculations. Defaults to EEVEE. May be a fast view, but will be slow to open with microscopy data, and is data-dependent.
  4. Rendered: Shows the scene as it will appear in the final render. By default, Microscopy Nodes sets this to be in Cycles. Often the best way to view microscopy data.

Further UI instruction (video)

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