What does the parameter 'dimension' means while 'generating a microscopic PSF'
When generating a PSF some choice must be made about the size. In most of the cases a border is added to avoid edge artifacts (padding). Depending on the purpose a choice can be made:
1-Ideal:
The size (in microns) of the generated PSF is determined from the physical size. Since the fringes of a PSF go on forever it is in theory not spatially limited, but in practice a volume can be chosen beyond which there is a negligible amount of energy from the PSF. The exception is the widefield PSF: there the amount of energy outside a volume around the focus is always infinite... As the intensity goes down locally it is possible to find a point at which the intensity of the PSF is well below the accuracy of any camera. Still, ideal WF PSFs are much larger than confocal or 2-photon ones.
2-Parent/Padded Parent/Full Padded Parent:
The size is derived from the Parent image: either exactly the same as the parent in fact no padding is made here, or as large as if the parent was 'padded'. The extra volume computed by the software is a trade-off between FFT (Fast Fourier Transform) compute efficiency and the size of the original image. For example If you have 31 layers in your image, adding one layer would optimize the Fourier Transform process. But adding one layer is not enough to prevent wrap around effects. The software will find out how many layers extra is a good compromise.
The Fully padded parent mode is relevant for widefield images, for other microscope types this is equivalent to Padded Parent.
If PSFs are to be compared it is best to use 'Parent' because that will fix the size.
3-Automatic:
A tradeoff is made between the physical size of the PSF and the memory requirement. In practice confocal or 2-photon ones are ideally sized; WF PSFs are smaller than ideal but at least as large as the padded parent.
4-Manual
You can manual set the number of Z-slices in this mode using the input field "Min XY-slices (Manual)". Widefield images should never be padded manually.
Keywords: padding generating psf
Categories: Faq Deconvolution, Huygens Faq, Imported Faqs
Platforms: Irix Linux
Related products: Hu Pro
