Working with z-stacks and 3d ROIs

How do I convert an Z-stack into something that can be used to detect volumes?

Thanks in advance.

Hi @cell789,

I’m not sure to understand what you mean ?
You need Z stack to do 3D measurements still you don’t necessary need 3D VTK view to do your analysis analysis. Plugin as HK-Means, Spot Detector, Thresholder… can work and generate 3D Rois even using the classic 2D view.

– Stephane

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Dear Matt,

Could upload an example image and tell us which structure you would like to detect?

As Stéphane said, you need a Z stack to do 3D measurements. It happens sometimes that 3D Z-stacks are interpreted by Icy as 2D stacks + time. I am wondering if this could be the case for you.

3D Z-stacks have a cursor on the left side of the viewer indicating the Z position you are at.
3D_Z-stack

2D stacks + time have a cursor at the bottom of the viewer indicating the frame you are at.

You can switch between each format by using the options Z/T conversion in the ribbon menu.

  • Use Convert to stack to convert from 2D stack + time to 3D Z-stack.

  • Use Convert to time to convert from 3D Z-stack to 2D stack + time.
    convert_to_time

Best regards,
Marion

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Thanks for the reply.

I guess my question boils down to when is HK Means detecting 3d volumes vs 2d areas. Manually working through my protocol it appears if you pass a z-stack to HK means it will create a volume. If you pass a single slice from the stack it will be 2D. To me it is not clear when I am working in 2D vs 3D.