Imported FAQs

• Does Huygens reads gzipped .ids files? Answer.
• How can I know whether there is a new version? Answer.
• Why is my Dos-window flashing? Answer.
• False Color in Expand Viewer is greyed out, why? Answer.
• Equalize Flux Reports Error. Answer.
• The label tool reports a 'Variable overflow' error; what to do? Answer.
• Error message `Failed to get main memory size' at startup 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.
• Is it possible to resize the image display side of the Operations window? Answer.
• How to fix a corrupt rpm database on Linux? Answer.
• Which causes resizing windows to be slow under RedHat? 8? Answer.
• Why do FlexLM tools fail with a Huygens license string? Answer.
• How far above and below the in focus information should I sample? Answer.
• Result after Fourier based convolution seems wrapped Answer.
• What are the pros and cons of piezo-electric vs step motor focusing control? 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.
• Can we put the license strings of all workstations into one file? Answer.
• What is the intended use of the noise generators? Answer.
• Do I need to use all three channels when observing through a broad bandpass barrier filter? Answer.
• Error messages after adding RAM in an SGI Octane Answer.
• Is it possible to crop a stack with the Huygens Pro? Answer.
• I had an error message while trying to label an image. What went wrong? 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.
• Can I download the latest version of Huygens while using my current license? Answer.
• Missing libCio.so Irix library, unresolvable symbol _'_nw'_HUl Answer.
• How to run Huygens or FluVR remote from a server? Answer.
• Can I install Huygens as non-root in a different location? Answer.
• We have 175 nm and 260 nm beads available. Which one to use? Answer.
• What do you mean by the mounting medium? Answer.
• How in the scripting can I open images in 16 bit signed and clip values greater than 32767? Answer.
• Shifted center of mass error message during PSF distillation Answer.
• Which pinhole size to use in case of mechanical hysteresis? Answer.
• What does this error mean when installing on Mac OS X fails? 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.
• Huygens won't install on RedHat? 9 Answer.
• Can we use very small beads in combination with averaging to obtain a PSF? Answer.
• Nyquist rate - What's arcsin/asin? Answer.
• Why do we want to center PSF's? Answer.
• Incorrect display of X-Z,Y-Z slices from Nikon ICS files in SFP renderer Answer.
• Crash when running Huygens Pro from Linux on a remote SGI 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.
• I can not share Tiff images between Linux and Windows XP. Answer.
• Averaging beads - image size criteria is to small. Answer.
• How to compute the back projected pinhole radius? Answer.
• Backprojected pinhole radius for Biorad confocals? Answer.
• The pinhole size of a measured PSF seems to have no effect on the the restored images. Why? Answer.
• Can I run Huygens Script from my PC remotely on a server? 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.
• Is there any way to read a 4D tiff image series into Huygens Essential or Huygens Pro? Answer.
• How much undersampling is still ok? Answer.
• Is there a z-step correction button for a measured psf? Answer.
• How do I limit the number of cpu used? Answer.
• What hardware to run Huygens on Linux or Windows? Answer.
• Can I deconvolve images acquired with a TIRF system? Answer.
• How to tune Huygens multiprocessing performance? Answer.
• How to tune multiprocessor performance with environment variables?. Answer.
• Is there a recipe for maximizing Huygens Pro performance for Xeon Processors? Answer.
• Heavy loaded processor during bead aligment procedure. Answer.
• Is there a suitable source of multi-wavelength micro-beads for PSF measurements? Answer.
• Can Huygens make use of multiprocessors? Answer.
• When shifting spheres, here always arose purple backgrounds!!! Why? Answer.
• I have heard that imaging diatoms is a difficult task, why? Answer.
• Should PSFs be produced for different wavelength when working in the visible light range? 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.
• Parameter check when loading an Imaris classic file into Huygens Answer.
• I can't find the PSF distiller; where is it? Answer.
• Does the Huygens read Leica NT LSM images? Answer.
• Does Huygens take advantage of the 64 bit functionality of the new G5 CPU's? Answer.
• Can Huygens save files as a "Multi-tiff" image? 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.
• Can I stretch intensity values? Answer.
• How to analyze images? Answer.
• What should be the total distance from the top to the bottom of the PSF? Answer.
• Huygens excludes all the beads while trying to reconstruct PSFs from beads taken in widefield mode. What is wrong? Answer.
• Error message when running Huygens Pro on a remote SGI Answer.
• What is the minimum data rate (Mbps) which will not slow down the graphics `too much'? Answer.
• Where can I find a listing of available beads ? Answer.
• My files are renamed and zero's added to the filename. Why? Answer.
• How should the acquisition zoom factor be taken into account in the calculation for the backprojected pinhole diameter? Answer.
• How can I download files from the SVI FTP server Answer.
• How to check the size of a bead as it appears in the image? Answer.
• Huygens fails to open some Zeiss LSM files, what can be the cause? Answer.
• Does the Huygens read 16-bit Tiff files? Answer.
• How do I do Colocalization Analysis in a multichannel image? Answer.
• How to measure a distance in an image? Answer.
• How can we see inside an object? Answer.
• What is more "dangerous" undersampling or oversampling? Answer.
• What is the refractive index of the embedding medium Vectashield? Answer.
• What is the refractive index of the medium? Answer.
• How serious a problem is undersampling in Z-direction? Answer.
• 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.
• What are typical speed values for fftw_test? 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.
• A raw 1 micron bead looks very elongated along the optical axis. Why? Answer.
• How do I install the Huygens on IRIX? Answer.
• What does the message "Huygens out of logical swap space' mean? 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.
• How can I reduce the size of the image with 'copy part of image'? Answer.
• Which wavelength do I have to set for multi-photon excitation? Answer.
• How to compute the Nyquist rate for an image? Answer.
• Huygens 2.3 does not start after installation of SCSL1.3 library Answer.
• Which pinhole size to use in the Leica SP2 confocal microscope? Answer.
• How to estimate the back projected pinhole value from the Airy Disk size? Answer.
• Does the PSF need to be re-measured when one changes the zoom? Answer.
• How to tune memory management on 64-bit Irix? Answer.
• Are multiple images from the same specimen needed at different focusing depths? Answer.
• How do I convert a collection of 2D files into a format the Huygens can deconvolve as a 3D stack? Answer.
• Error message about libscs_mp.so when starting Huygens 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.
• How can I create an ICS image from another program? FileI-ofRawDataImpFaq.
• How do I import images from Imaris into Huygens? Answer.
• Time Series: Why do you need to load the WHOLE time-lapse? Answer.
• Can the results of Huygens be imported back to the Leica-Software? Answer.
• I am not getting much compression of the z-blur with a measured PSF, why? Answer.
• The license string we received does not work. What can be wrong? Answer.
• Recommended books on Tcl/Tk? Answer.
• On which hardware platform runs Huygens fastest? Which benchmarks are available? Answer.
• How to check to whether or which version of SCSL is installed? Answer.
• How to write RGB Tiffs from scripts? Answer.
• What is an optimal sampling density in Z? Answer.
• When reading raw unsigned 16 bit integer data I run into problems with voxel values larger than 32767. How to deal with that? Answer.
• Huygens Pro on my SGI runs out of memory. How can I solve this? Answer.
• How to limit memory usage of Huygens Pro? Answer.
• How to calculate the X and Y sample sizes using a CCD camera. 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.
• Error when starting Huygens: unable to find libvk.so.1 Answer.
• Out of memory problem when generating a widefield PSF? Answer.
• Memory allocation error while running ICTM; what to do? Answer.
• Is virtual or logical swap space more important for Huygens? Answer.
• How to add swap space on Linux? Answer.
• How do I enable the use of shared memory on Linux? Answer.
• How can I increase the amount of memory Huygens can use under Linux? Answer.
• Should I oversample since the beads I'm using are only 175nm diameter? Answer.
• Where can I find references to the ICS file format? 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 it possible to start Huygens script from an UNIX shell passing the batch script to huscript as a parameter? Answer.
• What is a license entitlement? 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.
• How can I change the colors of the channels? Answer.
• Where can I find more references and support about deconvolution? Answer.
• How do I embed beads in water for PSF measurements? Answer.
• Do you know of any suitable solid mountants with suitable refractive indices? Answer.
• How can I install the Huygens on Linux-Debian? Answer.
• Does the pinhole size affect the Nyquist rate? Answer.
• When deconvolving 2-photon data what microscope type should we choose? 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.
• The PSF looks "banana-shaped" in the x-z or y-z planes. What could be the reason? 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 I have Huygens generate a debug or error log? Answer.
• How do you measure the Numerical Aperture (NA) from the experimental PSF ? Answer.
• How to immobilize a sample with agarose or gelatin 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.
• How to run Huygens from a remote workstation? Answer.
• How can I extend the memory usage on my Windows machine? Answer.
• MLE versus ICTM - Why is each method more effective under certain circumstances. Answer.
• What actual resolution improvement can be expected with Huygens? Answer.
• How do I install Cygwin to run Huygens remotely? Answer.

Special imported FAQs

• How does binning affect sampling? Answer.
• **?How does one compute the signal to noise ratio (SNR)? Answer.
• **? Which is the correct refractive index value? Answer.
• **?What is the value of blind deconvolution? Answer.
• Can I use lower Numerical Aperture lenses to obtain a larger field of view and still sample correctly? Answer.
• Does Huygens deconvolve Transmission images? Answer.
• Does the type of noise in an image affect the performance of the Huygens? Answer.
• Is deconvolution legitimate? Answer.
• Which pinhole size should I set for best results? Answer.
• Why is the effect of the deconvolution, especially in the axial direction so very poor? Answer.
• Updating Huygens Essential Windows XP fails, what can be wrong? Answer.
• **?Huygens reports that it can't find 'libscsl_mp.so' and other components. Why? Answer.
• Even after deconvolution my structure looks extremely elongated along the z-axis. Answer.
• What is the result of the "Sphere" button? Answer.