1. IMAGE INFORMATICS SOLUTIONS Extracting Information From Images Media Cybernetics UK 3D Training Session Part 1

2. Loading a 3D Volume 1.Load the images as a sequence into Image-Pro Plus 2.Select the 3D constructor from the Image-Pro “Advanced” file menu- This will prompt the dialog box opposite 3.Select, “load a colour sequence” or “individual colour channel” 4.Load the XY and Z voxel size – certain systems will automatically load this information 5.With large data sets it is best to sub sample our data 6.Select Auto – this gives its suggestion for the best sampling. Divide this suggestion by 4.

3. Viewing a 3D Volume Once the volume is loaded we have several options to view our stack. You can choose Blend, Sum or Max volume composition - these will give different effects depending on the background selected You can select to change the Global transparency to increase/decrease the intensities of the stack. You can also alter the Number of slices. 0 means Z is “as loaded.” Any low number gives you a lower quality image – this does however speed up rotation and response You can also apply Graduations and Axis

4. The 3D Constructor Window Hand – allows us to move our reconstruction Arrow - allows us to select objects in our reconstruction Eye – moves the selected object to the centre of the viewer Box – toggles between orthographic or perspective views Load New VolumeOpen options dialogChange background colour

5. Altering the Image Palette 1.When loading a 3D Volume, to get the best image we should adjust the opacity and colour spread. 2.We can also apply look up tables from the image or from preset tables 3.With multi channel images we can turn off selected channels 4.By checking Palette in the 3D Constructor options dialog box you will display the palette with the volume

6. Slicer 1.Tick Volume and Slicer in the option menu 2.The image displays the views in the xy, yz and xz plane (and the volume) 3.Select different positions in the 3 images, to see where certain particles are located in the different planes. 4.Toggle Interpolation and Transparent to show their effect 5.Select Thick Slices and increase the Thickness in the different directions. xyyz

7. Animation 1.Tick Volume and Animation in the option menu 2.Manipulate the volume in the 1 st position and select the red record button 3.Select the 2 nd position and select the red record button etc etc. (recommended to use the zoom as well for one of the positions). The brown indicators show the positions and the blue the calculation of the different frames in the animation. 4.Press the play button to see the animation and increase/decrease the Frames per camera position by pressing *2 or /2. 5.Unselect Animation Path to hide the indicators in the volume 6.Select the Create Animation in workspace button (icon on the far right, lower row. The animation in copied. Save the animation in IPP as an AVI-file

8. Ortho Slice 1.Tick Volume. In the top of the option menu select Ortho Slice and Add 2.Select Show handles, Y, Clipping 3.Select the hand icon on the right side of the image to manipulate the position of the volume. 4.Select the arrow (picker) on the right side of the image and select the handle bar to move up and down the clipping-plane 5.Change to X, to do the same 6.Select Transparent and Interpolation to make the cutting-plane clear and smooth.

9. Oblique Slice 1.Select Volume. In the top of the option menu select Oblique Slice and Add 2.Select Show handles, Interpolation, Clipping 3.Select the hand icon on the right side of the image to manipulate the position of the volume. 4.Select the arrow (picker) on the right side of the image and select the white bar to move up and down the clipping-plane. Select the grey handles to change the direction of the clipping plane 5.Select Transparent to make the cutting- plane clear