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Installation
Q: HASP -3 not found
A: The security dongle isn’t plugged in, isn’t recognized, or isn’t installed properly. Try each of the following:
- Make sure the black AutoQuant “HASP” dongle is plugged in.
- Remove the dongle from the computer and plug it back in.
- Try a different USB port.
- Got to Start->AutoQuant->AutoQuant X->Reinstall Dongle Drivers.
Q: HASP -10 (multi users)
A: Log off all users. If multiple users are logged on to the computer (fast user switch) for security reasons the program will not execute. This will also occur if you try to run AutoQuant software remotely.
Q: Why doesn’t AutoQuant X run on my 64bit computer?
A: You must install HASP’s 64bit USB dongle driver. This can be downloaded from:
http://www.aladdin.com/support/hasp/hasp4/enduser.asp
(this will be included in the X1.3 install automatically)
Crypt key doesn’t work either so you have download the 64bit patch off the website. This includes a new implementation of ApplicationGUI.dll and PlugInCore.dll that does not use Crypt key. Copy the dlls over the existing dlls in the AutoQuant program directory. The default location for this is at C:\Program Files (x86)\AutoQuant\AutoQuant X\ on 64bit machines.
Q: I get the follow error box during installation:
A: You are installing on a 64bit machine. New dongle drivers must be installed in order to run (see above). You can not run a demo copy of AutoDeblur X because we do not have a software security solution for Windows 64 yet. This is expected early in 2006.
Edit the AutoQuant X desktop shortcut by right clicking on it and going to properties. After the text in the Target edit box add /nodemo so it looks similar to this:
"D:\Program Files (x86)\AutoQuant\AutoQuant X\aqiPlatform.exe" /nodemo
Deconvolution
Q: How do I know what I am seeing is real?
A: Deconvolution is a powerful tool and can be used to recreate a representation of your data that is closer to the actual object being imaged. What you see and acquire is a misrepresentation. The microscope introduces blur, or flare, that makes details obscure each other. Deconvolution is an attempt to increase contrast, resolution and signal to noise through processing. For a more information please see “Clearing up Deconvolution”:
http://www.mediacy.com/aqi/pdf/BiophotonicsClearingUpDeconvolution%20Reprint.pdf
Deconvolution should improve your image quality. After deconvolution you may see things that you did not originally recognize but after careful examination of the original data you should see hints of the structures. Be weary of details that emerge because of deconvolution that are not present in the raw data.
Q: Out of memory Error
A: created the 1.2.2 patch that will work in most situations. If you aren’t running X1.2.2 please upgrade by going to Start->All Programs->AutoQuant->AutoQuant X->Check for Updates.
We also recommend setting the /3GB switch if it hasn’t already been done for your computer. This gives you access to the entire memory installed in your system. Here are step by step instructions on doing so:
1. Start->Control Panel
2. Open System Icon
3. Select Advanced Tab
4. Select Settings button in Startup and Recovery group
5. Select the Edit button to open boot.ini file
6. Add /3GB to the list of options after Windows=”Microsoft Windows…”
Here is a link to the Microsoft article that describes the process:
http://www.microsoft.com/whdc/system/platform/server/PAE/PAEmem.mspx
If this does not solve your problem please take a screen shot of the error message and send it to us. This will help us better diagnose where the problem is occurring. Can you also include the image parameters you are entering for deconvolution (xyz spacing, RI, NA, wavelength, and microscope modality). The image spacings may be too large which creates an enormous PSF that brings the system to its knees.
Q: How can I speed up my deconvolution?
A1: Decrease the size of the image through cropping. Even cropping by a small amount may decrease the number of subvolumes being used.
A2: Enabling “faster processing/reducted resolution” in the deconvolution dialog. This can increase processing time by as much as a factor of 4.
A3: Invest in more memory so less subvolumes are used. A faster processor would be the next hardware item to invest in.
Q: Why does my image look dimmer?
A: The light in the image is refocused to its source points, so the bright points are brighter, and areas that had previously appeared brighter due to the haze distribution are darker.
Q: Why is my data being subvolumed?
A: Deconvolution needs vast amounts of memory to process your data, frequently more than you have. The image is cut into subvolumes, deconvolved separately and then stitched back together.
Q: How can I reduce the number of subvolumes being used?
A: See “How can I speed up my deconvolution”.
Q: How do I reduce tiling artifacts resulting from subvolumes?
A: Subvolumeartifacts do crop up from time to time in noisy images or images with an uneven distribution of intensity. These artifacts can be reduced by increasing the subvolume overlap to 20 pixels in the Expert Settings dialog. This dialog can be accessed from the standard deconvolution dialog.
Q: How do I acquire an empirical point spread function?
A: Practice good imaging technicque as described in our tip “Garbage in Garbage Out” available on our website:
http://www.mediacy.com/aqi/tips_display.asp?id=4
Use sub resolution beads. 50 or 100nm beads work well and can be purchased from Molecular Probes (http://probes.invitrogen.com).
The PSF spacing does not need to be the same as the image spacing. It should be acquired at or with a finer spacing than when acquiring images. Ideally sample at half the Nyquist sample critera:
Nyquist xy = 0.6 * Emw / NA
Nyquist z = Emw / (4 * RI * sin2(sin-1(NA / RI) / 2))
The emissive wavelength (Emw) should be in nm. The resulting Nyquist sampling will be in nm.
You will most likely be imaging a field of beads. Crop out one bead that is isolated from the rest. Make sure that it is attached to the cover slip because beads that are free floating tend to move. When cropping the bead try to center it within the region being cropped. This does not need to be exact; our preprocessing is able to shift it by a few pixels.
When acquiring the PSF try not to saturate the brightest in focus slice.
For best results acquire a psf for each wavelength you are imaging with. You can create a multi channel dataset with a psf in each channel that can used for deconvolution.
For experts deconvolve an image with many beads in it with the “Save PSF” option checked in the deconvolution dialog. Use the saved PSF as the measured PSF. This will give you an average of all PSFs in the image.
General
Q: Computer requirements
A: Here are some current recommendations for 2006:
Minimum Requirements:
Intel Pentium 3 or similar AMD processor
1 GB Memory
Windows XP or 2000
1024x768 screen resolution
Recommend Requirements:
Intel Pentium 4 3GHz processor
4 GB Memory
Windows XP
1600x1200 screen resolution
nVidia GeForce 6600 or ATI Radeon 9800 Pro
Super Number Cruncher:
Dual Xeon 3.6GHz processors
4 GB Memory
Windows XP 64
nVidia QuadroFX 3000 or better
AutoQuant X can run on a 64bit processor but currently only does so in a 32bit mode. A special install is needed for 64bit computers and is available from our support staff. We hope to make the port to a true 64bit application once all our third party software tools and libraries have done so.
We can make use of the extended memory space up to the 4GB limit which is an added benefit of a 64bit system. More memory gives the most significant performance gain compared to processor speed and multiple processors. We plan to expand our ability to use more memory (8, 16, 32 GB or more) once we migrate to a 64bit application.
AutoQuant X is multi-threaded and will make use of hyper-threading, dual core, and dual processor technology. This makes it possible to run two or more deconvolutions or other operations at the same time. Since deconvolution is a memory intensive operation many jobs will use all available memory for processing leaving no memory for a second deconvolution. Dual processing will still give the added advantage of having a second processor free for visualization, file i/o and other lower priority operations.
We make use of 2D and 3D textures when doing 3D visualization. The more texture memory a graphics card has the better. Current high end gaming cards are coming with 256MB of graphics memory, the very best with 512.
Q: Why isn’t the viewer working, my menus refreshing?
A: Update your graphics drivers.
Q: How do I upgrade?
A: If your computer is connected to the internet go to Start->All Programs->AutoQuant->AutoQuant X->Check for Updates. If the computer where AutoQuant X is installed is not connected to the internet contact AutoQuant support (support@aqi.com or 301-495-3305) to obtain a patch.
Q: Does AutoQuant run on 64 bit computers?
A: Yes but with a few modifications see “Why doesn’t AutoQuant X run on my 64bit computer?”
Q: I’m missing menu items that once used to be there.
A: The menu configuration file has become corrupt. Delete the aqiPlatform.exe.config.xml found in the AutoQuant X program directory. The default location for this is C:\Program Files\AutoQuant\AutoQuant X.
Q: How do I import Leica formatted file sequences?
A: Go to File|Ope nand navigate to the folder where the TIFF files that are associated with the .lei file reside. Select one of the TIFF files. At the bottom of the dialog, check the box marked “Use Sequence Detection”. That should cause the filename to appear at the bottom with dropdown menus in place of the sequence locations. Use the dropdowns to specify what the sequences are. Then press open, and the datasets should load as multichannel volumes.
5D Viewer
Q: I don’t see anything in the 5d Viewer, the viewer fails to load, the performance is poor, or the image looks incorrect.
A: Many times the graphics drivers installed on a computer are out of date. Visit the chip manufacturer to download and install the latest drivers. You should also set the Hardware Acceleration to Full by going to Start->Control Panel->Display->Settings->Advanced->Troubleshoot.
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