FAQ's about deconvolution

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• Equalize Flux Reports Error. Answer.
• What are the internal magnifications of the Biorad 1024 and the Biorad Radiance? Answer.
• What's a bandlimited system? Answer.
• Is there a way to either turn scaling off or to predefine a scaling value? Answer.
• How far above and below the in focus information should I sample? Answer.
• Result after Fourier based convolution seems wrapped Answer.
• How critical is the difference between the nominal size of the microsphere and its actual size? Answer.
• What is the potential danger to apply the non-negativity criterion between iterations? Answer.
• What is the intended use of the noise generators? Answer.
• Is the dimension after deconvolution fixed according to voxel dimension/aspect ratio? Answer.
• Literature reference on widefield and confocal Nyquist rates? Answer.
• How close may beads be to the image edge before they are rejected? Answer.
• Can I compare the quality factor and the I-divergence between different images? Answer.
• We have 175 nm and 260 nm beads available. Which one to use? Answer.
• Shifted center of mass error message during PSF distillation Answer.
• Which pinhole size to use in case of mechanical hysteresis? Answer.
• Can I deconvolve a single Tiff image? Answer.
• May I clip bright pixels which dominate the scene? Answer.
• Is the sampling rate a function of the structure that you're modeling? Answer.
• Measuring beads - apart from the bead size is there anything else we miss? Answer.
• Is the SNR limited to 16 in 8-bit photon counting? Answer.
• What SNR would you suggest for widefield images? Answer.
• What is an undersampled stack of images? Answer.
• Can we use very small beads in combination with averaging to obtain a PSF? Answer.
• Why do we want to center PSF's? Answer.
• Can artefacts due to unstable laser power be removed by deconvolution? Answer.
• How should I interpret the Quality factor? Answer.
• Why can I not compute a PSF for a 'Generic Sensor' image? Answer.
• Averaging beads - image size criteria is to small. Answer.
• The pinhole size of a measured PSF seems to have no effect on the the restored images. Why? Answer.
• What does the message: 'total reflection at glass/medium interface (...)' mean? Answer.
• Can confocal reflection images be deconvolved? If so, how? Answer.
• What does 'stepsize' mean? Answer.
• How much undersampling is still ok? Answer.
• Is there a z-step correction button for a measured psf? Answer.
• Can I deconvolve images acquired with a TIRF system? Answer.
• Heavy loaded processor during bead aligment procedure. Answer.
• I have heard that imaging diatoms is a difficult task, why? Answer.
• What emission wavelength to use to represent the detected spectrum? Answer.
• Can I deconvolve a single plane widefield image? Answer.
• Do you have to generate individual PSF's for each channel? Answer.
• I can't find the PSF distiller; where is it? Answer.
• What to use as excitation wavelength: laser line or fluorescence spectrum peak Answer.
• In Huygens Pro there are two tools to measuring a PSF from latex beads. Which to use? Answer.
• How does Huygens Professional derive a Point Spread Function? Answer.
• How to analyze images? Answer.
• What should be the total distance from the top to the bottom of the PSF? Answer.
• Where can I find a listing of available beads ? Answer.
• How should the acquisition zoom factor be taken into account in the calculation for the backprojected pinhole diameter? Answer.
• How to check the size of a bead as it appears in the image? Answer.
• What is more "dangerous" undersampling or oversampling? Answer.
• What is the refractive index of the embedding medium Vectashield? Answer.
• How serious a problem is undersampling in Z-direction? undersampling.
• Photon counting - why do people sometimes question its practicality? Answer.
• How deep down (what Z depth) the Huygens would restore 2-photon data. Answer.
• Where do I need to setup Huygens Essential for use with a 2-photon system? Answer.
• Any suggestions on setting pinholes for spinning disc systems? Answer.
• Which Huygens optical option is best for the Perkin Elmer Ultra View? Answer.
• What to take for the Z-sampling, the nominal or foreshortened distance? Answer.
• MLE versus ICTM - Will one method be faster or more rigorous or give a better quality result? Answer.
• Why do I have to center a PSF? Answer.
• Which wavelength do I have to set for multi-photon excitation? Answer.
• How to compute the Nyquist rate for an image? Answer.
• Does the PSF need to be re-measured when one changes the zoom? Answer.
• Are multiple images from the same specimen needed at different focusing depths? Answer.
• When is the RI / NA combination correct? Answer.
• What does the parameter 'dimension' means while 'generating a microscopic PSF' Answer.
• What is the computation time for deconvolving an image? Answer.
• What is the quick and dirty way to estimate the SNR in the image? Answer.
• Time Series: Why do you need to load the WHOLE time-lapse? Answer.
• I am not getting much compression of the z-blur with a measured PSF, why? Answer.
• What is an optimal sampling density in Z? Answer.
• How to limit memory usage of Huygens Pro? Answer.
• Can a small sphere like object deconvolved down to a sphere again? Answer.
• Can a 2D-time series be deconvolved as 3D stack? Answer.
• Should I use 175 nm or 260nm diameter beads to measure the PSF? Answer.
• What is the difference in sampling between widefield and confocal microscopes? Answer.
• Out of memory problem when generating a widefield PSF? Answer.
• Memory allocation error while running ICTM; what to do? Answer.
• Should I oversample since the beads I'm using are only 175nm diameter? Answer.
• How do I compute the correct sampling for 2-Photon imaging? Answer.
• How to compute the Nyquist rate with 2-photon excitation? Answer.
• What is the potential drawback of estimating the signal to noise ratio (SNR) to high? Answer.
• What is the potential drawback of estimating the signal to noise ratio (SNR) to low? Answer.
• Is deconvolution on 2D or 2D-time images possible? Answer.
• Is it possible to deconvolve brightfield images? Answer.
• Skipping channels in deconvolving with Huygens Pro? Answer.
• Where can I find more references and support about deconvolution? Answer.
• How do I embed beads in water for PSF measurements? Answer.
• Does the pinhole size affect the Nyquist rate? Answer.
• How to estimate the signal to noise ratio? Answer.
• Are there batch processing scripts available? Answer.
• What is the maximal voxel size at which Huygens can still do a good job. Answer.
• Why do my deconvolved images look darker than the raw images? Answer.
• Is there a mismatch between the refractive index of the bead and the surrounding medium? Answer.
• Can we use 1 micron beads for PSF measurements? Answer.
• Which deconvolution method to use in the Pro? Answer.
• How do you measure the Numerical Aperture (NA) from the experimental PSF ? Answer.
• What are the characteristics of the Confocal, Widefield, Multiphoton (and other) modules? Answer.
• Should the sampling density used in PSF measurement be equal to the of the specimen? Answer.
• The better sampled the PSF, the better the deconvolution result? Answer.
• MLE versus ICTM - Why is each method more effective under certain circumstances. Answer.
• What actual resolution improvement can be expected with Huygens? Answer.