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
• Fast hard drive• Video card with 128+ MB
– Good gaming card (nVidia or ATI)
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.
Opening a single file• Select File | Open
Select datasets associated with the current file here
Shows dimensions of current dataset
Note: The dataset header file is now stored as an XML. X will read the old AQH header files.
Opening a multi-file dataset
2: Check here to activate the automatic sequence detection
1: Select the first file
3: Change the detected sequence dimensions as necessary
The new dataset name will have a ‘#’ for each numeric sequence used
New dimensions shown for Depth and Time Points
4: Open the new dataset
Importing multi-channel files• When the files are not numbered by channel
2: Select channel file
1: Check here to build multi-channel dataset
3: Add channel to dataset (Go to Step 2 as required)
4: Set channel color
5: Set dataset name
6: Open dataset after all channels added
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
Image Display
Workspace
Batch
Image display• Maximum Projection by default (Min for brightfield)
Time controls
Zoom Controls
YZ Projection Tab
Max Projection
XZ Projection Tab
Slice (Z) controls
ROI SelectionSlice View
More image display• Click on XZ and ZY tabs
Triple Maximum Projection Triple Slice Viewer
Data Manager• Shows all loaded datasets• Double click to bring up image display
Active dataset
Click ‘+’ to reveal dimensions
Uncheck Time Points or Channels to be excluded
Click pin/unpin dialog
Right-click dataset for menu items
Dataset parameters
• 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
DimensionsSummary
Channels InstrumentInfo
Close dataset
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
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
Top 8 colors
Non-linear look-up tables
Visible wavelength spectrum
Change channel color
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
Select existing probe/wavelength from here under Summary tab
Define new probe and wavelength under Channels tab
Define channel name
Disable channels from display and processing by unchecking here
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
Other dataset information
• Simply enter specimen name, dataset collector and any other notes
Brightness/ContrastReveal Image Enhancement control here. Close when finished
Minimum intensity threshold
Maximum intensity threshold
Gamma
Apply/Reset values for all time-points
Apply to All Channels, or select individual channels
Click Y-Axis to toggle Linear-Log scale
Automatically set thresholds to dynamic range for each channel
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
3D Deconvolution• Start with theoretical settings
Method: Adaptive PSF (Blind)PSF Settings: Theoretical PSFDeconvolution 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
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
processingCan be moved back if not already launched
• A specific Start time can be set using time at top of dialog
Add to Pending Operations
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: [email protected]
phone: +1 (301)-495-3305
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