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 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.

5. 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

6. 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

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 Image Display Workspace Batch

8. 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

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

10. 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

11. 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 Dimensions Summary ChannelsInstrument Info 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 Top 8 colors Non-linear look-up tables Visible wavelength spectrum Change channel color

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 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

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 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

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.comtechsupport@mediacy.com phone: +1 (301)-495-3305