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simone milan
Oct 5, 2017, 6:57:42 AM10/5/17
to Icy imaging
Hello,
I have a question about the spot detector program: when I use the program to analyze a Z stack image composed by 65 stacks, I have an error on the XLS output file that says: "error scale". I tried to change the scale setting (from 2 to 5 so from 3pxl up to 25pxl) but the error remains. How can I solve this problem? If I do the same with an image composed by less stacks (16) i don't have the error.
Can I just ignore the sentence or i need to fix some parameters? The analysis seems to be reliable.
Fabrice de Chaumont
Oct 9, 2017, 12:48:35 PM10/9/17
to Icy imaging
Hi
This message usually comes when you set scales that are too high for the resolution of your image, and typically the resolution in Z.
The formula is 5+(int)(Math.pow(2, numScales-1))*4 ( B3SplineUDWT.java line 100.)
In the following table you have the scale and the min XYZ needed:
For scale 5 in 3D you need at least 69 Z to process. And this will consume a lot of memory.
This tables shows that big scales are not recommended. If you end up to such need, maybe you should pre process your images or use another method.
You can set "force 2D wavelets" so the wavelets will be computed only in X and Y and you should have enough pixels. This will work with any number of Z in your stack. This tends to seperate the planes, which may not be the effect you are looking for.
Note: when the soft says "detect 25 pix at scale 5" it actually needs more Z to process it.
Fabrice
This message usually comes when you set scales that are too high for the resolution of your image, and typically the resolution in Z.
The formula is 5+(int)(Math.pow(2, numScales-1))*4 ( B3SplineUDWT.java line 100.)
In the following table you have the scale and the min XYZ needed:
| 1 | 5 |
| 2 | 9 |
| 3 | 21 |
| 4 | 41 |
| 5 | 69 |
| 6 | 105 |
| 7 | 149 |
| 8 | 201 |
| 9 | 261 |
| 10 | 329 |
For scale 5 in 3D you need at least 69 Z to process. And this will consume a lot of memory.
This tables shows that big scales are not recommended. If you end up to such need, maybe you should pre process your images or use another method.
You can set "force 2D wavelets" so the wavelets will be computed only in X and Y and you should have enough pixels. This will work with any number of Z in your stack. This tends to seperate the planes, which may not be the effect you are looking for.
Note: when the soft says "detect 25 pix at scale 5" it actually needs more Z to process it.
Fabrice
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