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Table of Contents

I) Adding an object to the 3D scene

1) Open the object list (Lists → Object List OR shift + CTL + o)

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2) Inside the object list, right click on the object you want to add to the 3D scene → 3D → Add to scene

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3) A separate 3D scene window containing a 3D reconstruction of your object should open (note – if a window does not appear, check behind your PyReconstruct window):

You can add multiple objects to the same 3D scene
An selected object in the 3D scene will be indicated in the top left corner.
Hovering your cursor over different parts of the 3D object will display the corresponding section number and X-Y Coordinates in 3D space
Double clicking on a point on your 3D object will navigate you to the corresponding point in your 2D scene window

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II) Removing an object from the 3D scene
1) Right click on object in object list → 3D → Remove from scene	Image Modified

III) Editing 3D object
1) Edit object 3D scene attributes by right clicking on object in object list → 3D → Edit 3D settings	Image Modified
2a) A 3D object settings window will open. Here you can change the 3D type and opacity (how transparent your object is). For most objects you will want 3D Type: Surface. However, for some object types you may want to select 'spheres' or 'contours' (see 2b, 2c)	Image Modified Image Modified
2b) For vesicles, you will want to change your 3D Type to spheres	Image ModifiedImage Modified
2c) In some cases, you may want to view your object's as its 2D contours stacked in 3D.	Image ModifiedImage Modified
3) To change the color of your object in the 3D scene you need to change your object attributes: Right click → Edit attributes. --Note the object will need to be removed from the 3D scene and added back in if you want your 3D scene window to reflect the attribute changes	Image ModifiedImage Modified

IV) Navigating the 3D scene window (Scale Cube, Obj Transparency)

1) Access the 3D scene help menu: Click on 3D scene window → press shift + ? key

This help window will show you all the important hotkeys that you will need to navigate the 3D scene window

Highlights

How to add/edit a scale cube
- Press c key on keyboard to toggle on/off
- Change scale cube side-length/color: right click on scale cube
- Use left/right/up/dow arrow keys to move scale cube in XY
- Use ctl + up/down to move scale cube in Z
How to change object transparency in 3D scene
- Object transparency can either be edited in 3D scene settings (see part III on Editing 3D object)
- OR by using the square bracket keys:
  - Decrease opacity (make object more transparent): Left square bracket key: [
  - Increase opacity (make object less transparent): Right square bracket key: ]

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V) 3D scene smooth settings
1) 3D scene smoothing type/method used by PyReconstruct can be change by going to Series → 3D → Change smoothing type	Image Modified
a) Humphrey (less smooth)	Image ModifiedImage Modified
b) Laplacian (most smooth)	Image ModifiedImage Modified
c) None (blocky)	Image ModifiedImage Modified

Versions Compared

Old Version 13

New Version Current

Key

I) Adding an object to the 3D scene

II) Removing an object from the 3D scene

III) Editing 3D object

IV) Navigating the 3D scene window (Scale Cube, Obj Transparency)

V) 3D scene smooth settings