Customizing Z-stacks and 3D rendering

Hi everyone,

I am having problem with the 3D rendering of a z-stack.

I upload the TIFF photos (40) and Icy immediately create the stack.
The problems are that I do not know how to customize my stack:

  1. where can I select the distance between the images? Because when I try to do the 3D rendering, the image is totally flat.
  2. how to change the intensity of the channels in the stack?

Thanks a lot for your help.

Federica

Dear Federica,

  1. to change the Z spacing, you can edit the metadata in the Sequence properties pane (click on Edit and change the Z pixel size).
  2. to adjust the contrast and brightness, select the channel of interest in the Histogram and colormap pane and play with the red and blue cursors.

Best regards,
Marion

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Dear Marion,
thanks a lot for your answer.
I have tried but I still have some problems:


As you can see from the image, even if I have put y and x axis length of 1306 um a d 1742 um respectively, the measure on the 3D view are totally in a different scale.
What have I done wrong?
Thank you

Dear Federica,

To be sure I get your issue: you expect the units on the 3D view to be in millimetres (mm) as the pixel size in your sequence properties, and not in 10^6 micrometres, right?

It looks like the units choice on the 3D OrthoViewer is hard coded in micrometres. I am inviting @drdaleks, the main developer of this tool and @Stephane the lead developer of Icy to join this discussion and give their opinion on that.

Best regards,
Marion

Dear Federica,

Be careful, the indication you have to give is the pixel size and not the axis length.
I guess your X and Y pixel size are the same but you need to take care about the Z pixel size. Almost time Z pixel size is different (because of the microscope Z resolution) so check out the Z step of your acquisition to fix the Z pixel size information then your 3D stack will have correct proportions on screen :slight_smile:

Best,

– Stephane

Thanks @MarionLouveaux for your directions.
I have changed some different things in the days, thanks to @Stephane suggestions, thanks a lot!
Just a little question regarding the z-axis: if I know that the Z step is 17.3 um, do I have to assume that each image has a height of 1 pixel and putting 17.3 as the Z pixel size?

Thanks again.
Best,
Federica

Yeah, each Z slice (1 pixel thin) correspond to a single Z step, so you should set 17,3 um as value for pixel size Z.
But you also need to fix the X and Y pixel size (the size for a single X/Y pixel) otherwise your image won’t look correct.

Best,

– Stephane

Now I have set all the pixel sizes on the different axes, thanks a lot for your support!
Best,
federica

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