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How to use the render plane manipulator

Summary

The render plane manipulator allows you to interactively position the plane being visualized in the napari Image layer plane depiction mode. The plane depiction mode is a 3D rendering mode where only the specified plane is rendered. This is a power rendering mode for visualizing structures within a 3D volume, but defining the precise plane programatically can be challenging. Thus, the render plane manipulator is useful for interactively positioning the rendering plane.

Instructions

  1. Launch napari. Open your terminal and activate your napari-threedee environment. Enter napari in the command prompt to launch napari.

    napari
    
  2. Load the "HIV virus-like particles tomogram" image from the File menu: File -> Open Sample -> HIV virus-like particle tomogram. Note that this will download the sample image so it make take some time. If you have previously opened the sample image, it should be cached and will not download again.

    screenshot of the hiv tomogram

  3. Click the "Toggle ndisplay" button in the lower left corner of the viewer to enter 3D rendering mode.

    toggle ndisplay button

    Upon clicking the button, you will see the volume in 3D. You you can click and drag to rotate the view. Note that the HIV particles are visible, but low contrast.

    particles rendered in 3D

  4. In the layer controls, change the depiction mode from volume to plane.

    depiction mode dropdown.

    After changing the depiction mode, you will see a single plane being rendered from your 3d volume.

    plane rendering mode

  5. Open the render plane manipulator plugin from the menu: Plugins -> napari-threedee -> render plane manipulator. You will see the render plane manipulator appear on the rendering plane.

    render plane manipulator

  6. You can click and drag the translator on the manipulator to translate the plane along its normal.

  7. You can click and drag the rotator to rotate the plane around the manipulator.

    If you would like to change the center of rotation, you can press the shift key while clicking on the plane with the left mouse button to move the manipulator.