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: techsupport@mediacy.com

phone: +1 (301)-495-3305