Customizing Z-stacks and 3D rendering

Image Analysis
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#1

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

#2

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.

GUIsidepane
GUIsidepane3770×2513 2.13 MB

Best regards,
Marion

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#3

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

image
image1917×808 257 KB

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

#4

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

#5

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

#6

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

#7

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

#8

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

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