Why do my deconvolved images look darker than the raw images?
The deconvolution process increases the → Dynamic Range of the dataset, i.e the intensity range increases.
The images are shown on the screen adapted to the whole intensity range. A computer screen can not display arbitrarily high intensities, there is a maximum for the brightness of a pixel in the screen. Therefore the maximum intensity in an image is normally mapped to the maximum intensity a screen can display, and all the other pixels in the image are scaled accordingly.
Since the image is auto-scaled between the maximum and minimum intensity when displayed on the screen, the background features will appear darker. If you have a very bright point somewhere in the image, almost any other feature will show very dim. It is as if you where dazzled by the bright feature.
You may use the gamma button to highlight the darker features in the image, giving higher weigth to the representation of the lower intensities.
That is an expected result. Still, if you suspect that something may be wrong on your deconvolution, you can check your Point Spread Function (PSF). It may happen, for example, that the PSF is calculated based on wrong parameters or distilled out of beads that were not acquired in the same conditions of the image. If the PSF is too large, deconvolution will remove many features that are interpreted as wrong objects. (Mind that anything in the image smaller than a PSF shouldn't be there in the restored image and will vanish: the PSF is the image of a single mathematical point, and nothing in the restored result can be smaller than that). You are advised to double-check the size of the PSF that you are using, and compare it with the size of the features in your image and with a theoretical PSF that you can manually calculate in Huygens Professional or using our Nyquist Calculator on-line tool.
This effect increases with higher SNR
What is explained above means that, if for any reason, you have a very bright pixels somewhere in your image, all the other pixels will look relatively dim. (That's how things actually are!!! All other pixels in the image are dim, relative to the brightest one). The brighter and brighter you make this special pixel, the dimmer and dimmer will the others look.
By increasing the SNR in the deconvolution you are also allowing more light to be gathered to their source pixels, increasing the deblurring effect of the restoration. This will of course change the relative intensity between bright and dim pixels, making the image look dimmer in most places.
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Keywords: dynamic range intensity gamma dark image<br>
Categories: Faq Deconvolution, Faq Visualization, Huygens Faq, Imported Faqs<br>
Platforms: Irix Linux Windows AIX<br>
Related products: Hu Ess Hu Pro<br>
