Getting Started with

blessinghomoeopathAI and Robotics

Nov 30, 2013 (3 years and 11 months ago)

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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 Selection

Slice 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

Dimensions

Summary

Channels

Instrument

Info

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/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

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 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

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

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