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Getting Started with AutoDeblur X

Getting Started with AutoDeblur X. System Requirements. Windows 2000/XP or Windows x64 .NET 1.1 framework will be installed by X 1 GB of RAM (2GB+ recommended) Support for 3GB switch, 4GB with Win64 Fast processor, lots of cache Dual processor support Intel Pentium 4/Xeon recommended

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Getting Started with AutoDeblur X

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  1. Getting Started with AutoDeblur X

  2. System Requirements • Windows 2000/XP or Windows x64 • .NET 1.1 framework will be installed by X • 1 GB of RAM (2GB+ recommended) • Support for 3GB switch, 4GB with Win64 • Fast processor, lots of cache • Dual processor support • Intel Pentium 4/Xeon recommended • Fast hard drive • Video card with 128+ MB • Good gaming card (nVidia or ATI)

  3. Starting the program • Make sure your dongle is plugged in and the red-light is on - If not, remove the dongle, and go to: Start | All Programs | Media Cybernetics | AutoDeblur & AutoVisualize X | Reinstall dongle drivers - Plug the dongle back in • Start AutoDeblur and AutoVisualize X from the desktop icon or menu: Start | All Programs | Media Cybernetics | AutoDeblur & AutoVisualize X | AutoDeblur and AutoVisualize X • The splash screen will appear and scan through the plug-ins in the directory. This may be slower the first time the program is run.

  4. Opening a single file Select datasets associated with the current file here • Select File | Open Shows dimensions of current dataset Note: The dataset header file is now stored as an XML. X will read the old AQH header files.

  5. Opening a multi-file dataset The new dataset name will have a ‘#’ for each numeric sequence used 1: Select the first file New dimensions shown for Depth and Time Points 4: Open the new dataset 2: Check here to activate the automatic sequence detection 3: Change the detected sequence dimensions as necessary

  6. Importing multi-channel files • When the files are not numbered by channel 3: Add channel to dataset (Go to Step 2 as required) 1: Check here to build multi-channel dataset 4: Set channel color 2: Select channel file 5: Set dataset name 6: Open dataset after all channels added

  7. Drag-and-drop into X • Drag single or multiple files from Explorer - Drop in Data Manager, Workspace or Batch region • Each file is opened as a separate dataset - In Data Manager and Workspace, a single file will also have the image display generated - Multiple files are loaded with display suppressed to save time - Batch only loads the dataset Data Manager Batch Image Display Workspace

  8. Image display • Maximum Projection by default (Min for brightfield) Zoom Controls Max Projection Slice View ROI Selection YZ Projection Tab Slice (Z) controls XZ Projection Tab Time controls

  9. More image display • Click on XZ and ZY tabs Triple Maximum Projection Triple Slice Viewer

  10. Data Manager • Shows all loaded datasets • Double click to bring up image display Click pin/unpin dialog Active dataset Right-click dataset for menu items Click ‘+’ to reveal dimensions Uncheck Time Points or Channels to be excluded

  11. Dataset parameters Dimensions Channels Instrument Summary Info • Set parameters quickly on Summary Tab or in more detail on other tabs • White regions editable • Click ‘Apply’ or outside cell to enter values • Values will be auto-formatted • Add new probes under Channels tab • Add new lenses from Instrument tab Close dataset

  12. Setting Spacings • Spacings can be entered directly in Summary tab in several forms “.364 .357 .4” “0.364 0.357 0.4” “0.364 x 0.357 x 0.4 um” “364 x 357 x 400 nm” • Values will be auto-formatted • Can also be entered in Dimensions tab • Spacings can also be calculated using theoretical or calibrated values

  13. Setting channel colors • Set channel colors from drop-down menu • Look-Up only available for single channel • Once Wavelength used, future changes in probe wavelength will change color Change channel color Top 8 colors Non-linear look-up tables Visible wavelength spectrum

  14. Setting channel wavelength • Select existing probes from Summary tab • Type ‘Probe (wavelength)’ directly in Summary tab • Add new probes to database under Channels tab • If no channel Name, then Probe or Wavelength used Disable channels from display and processing by unchecking here Define new probe and wavelength under Channels tab Select existing probe/wavelength from here under Summary tab Define channel name

  15. Instrument settings • Select predefined objective lenses in Summary tab • Immersion medium will be automatically set if defined • Define new objective lens in Instrument tab and add to database • Lens name will be automatically created • Recommended (Nyquist) spacings calculated using shortest wavelength

  16. Other dataset information • Simply enter specimen name, dataset collector and any other notes

  17. Brightness/Contrast Reveal Image Enhancement control here. Close when finished Click Y-Axis to toggle Linear-Log scale Gamma Minimum intensity threshold Maximum intensity threshold Apply to All Channels, or select individual channels Automatically set thresholds to dynamic range for each channel Apply/Reset values for all time-points

  18. Operation status • All processing goes through a multi-threaded operation queue. Supports multiple CPU’s • View | Display Status will show operations • Right-click to Show Details, Cancel or Clear Completed operations • Expand operation task to see sub-tasks • Minimize Status when not required for better speed and increased viewing area

  19. 3D Deconvolution • Start with theoretical settings Method: Adaptive PSF (Blind) PSF Settings: Theoretical PSF Deconvolution Settings: Use Default • Optics Information • Indicates if Setting are OK • Change values in Data Manager • Subvolume Information • Indicates available memory and number of subvolumes • Minimize/close applications to increase memory and reduce subvolumes • Subvolume/Memory Info not as applicable if deconvolution is already running Start Now Add to Batch

  20. Batch Viewer • Open Batch Viewer from or from View | Task Batch • Add items to batch by: Drag/drop from Data Manager or Explorer Batch button in dialog box • Select Task from drop down if unset • Green  indicates valid settings • Right-click for copy/paste • Highlight multiple datasets to duplicate settings easily • Move to pending area to queue up processing Can be moved back if not already launched • A specific Start time can be set using time at top of dialog Add to Pending Operations

  21. Need more information? • Go through the quick start guides • Read the manual (PDF file included in install) • Go through the tutorial examples • Go to our Website: http://www.mediacy.com/aqi/index.asp • Contact Media Cybernetics Support: email: techsupport@mediacy.com phone: +1 (301)-495-3305

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