Argus-20 Reference Manual

 
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Argus-20
Reference Manual

                            Improvision,
                      Viscount Centre II,
   University of Warwick Science Park,
                      Millburn Hill Road,
                     Coventry. CV4 7HS
             Tel: 0044 (0) 24 7669 2229
            Fax: 0044 (0) 24 7669 0091
       e-Mail: admin@improvision.com
   Internet: http://www.improvision.com
Printing History

              Edition                              Date

              Edition 1                            December 1997

              Improvision believes the information in this manual to be correct at the date of issue.
              However, it is subject to change at any time and does not represent a commitment on
              the part of Improvision. Improvision shall not be liable for errors contained herein or
              for incidental or consequential damages in connection with the furnishing,
              performance, or use of this manual. Improvision has a policy of continual
              development and reserves the right to change information within this manual without
              notice to reflect changes in the systemÕs design and specification.

              © 1996-1997 Improvision, Image Processing & Vision Company Limited.
              All rights reserved.

              Copyright Notice
              Apple, Finder and Macintosh are registered trademarks of Apple Computer, Inc.
Argus-20

                                                                                                                    Argus-20

Overview

           This module provides support for the Argus-20, HamamatsuÕs image processing
           computer, which allows you to apply a wide range of processes/effects to video
           images in real-time. There are two connections from the Argus-20 computer to the
           Macintosh which is running the Openlab software.
           n       The video connection which allows the Macintosh to display the effects of the
                   Argus-20 processes on the real-time video images on the screen. This channel
                   connects the Video Output port on the Argus-20 to the video input port on the
                   Macintosh; this may be to built-in video or to a separate video card in the
                   Macintosh.

           n       The SCSI connection which is the main data channel. It is used to transfer the
                   high quality digital images produced by the Argus-20 processing to the
                   Macintosh, and also to pass commands and status information between the two
                   units.

           This guide describes how to set up and use OpenlabÕs Argus-20 module. The diagram
           on the following page illustrates the cabling between the two units.

Contents
           Overview......................................................................................................................... 1
           Contents ......................................................................................................................... 1
           Argus-20 Cabling............................................................................................................ 2
           Argus-20 Preferences .................................................................................................... 3
           The Argus-20 Palette...................................................................................................... 5
           Using Openlab to Control the Argus-20.......................................................................... 6
           Processes ..................................................................................................................... 10
           Contrast Enhancement ................................................................................................. 18
           Post-Processing ........................................................................................................... 23
           Hints and Tips .............................................................................................................. 24
           The Argus-20 and Automator tasks.............................................................................. 26
           Automation - Hints and Tips ......................................................................................... 43
           An Example Automation ............................................................................................... 43
                                                                                                                              Argus-20        1
OPENLAB

      Argus-20 Cabling

                   The Video connection may be to either the built-in video port or to a separate card in
                   the Macintosh.

                   IMPORTANT! Make sure that both units are switched off before you attach the SCSI
                   cables, and always switch on the Argus-20 computer before you switch on the
                   Macintosh.

                                                                                  Macintosh

       Argus-20
                           SCSI                                                 SCSI
        VTR

                                To Video-In on Mac       either built-in

                                                         or separate card

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Argus-20

Argus-20 Preferences

               Openlab gets most setup information, such as the board rate, directly from the
               hardware. However, before you can start to use the Argus-20 with Openlab, there are
               a few preferences that you need to set up, to ensure that the Argus-20 computer and
               the Macintosh are running in step with each other. If you do not set up the
               preferences, you may get unexpected results.

               Standard cameras

         1.     Select Preferences... from the Edit menu.

         2.     Click on the Argus-20 icon in the left-hand column.

          3.   Click on the Resolution pop-up menu and select a microscope from the list.

                                        Refer to the Argus-20
                                        manual for further
                                        information about
                                        resolutions

                                                                                        Argus-20       3
OPENLAB

               4.   Click on the Video Source pop-up menu and select the appropriate video source from
                    the list.

                                                                     Choose the option
                                                                     which is appropriate for
                                                                     your video camera

               5.   Click on the Video Sync. pop-up menu and select the appropriate option from the list.

                                        The available options
                                        will depend upon the
                                        video source

               6.   Click on Save to save your choice and restart Openlab. It will take Openlab
                    approximately 10 seconds to reset the Argus-20 for the new values.

                    Note: Only use the Reset Argus button if instructed to do so by an Improvision or
                    Hamamatsu engineer. It will reset the camera to its default values.

                    Cameras that Support Frame Integration

                    If you select a camera that supports frame integration at step 4, you will find that there
                    is an extra section on the Argus-20 palette. This allows you to define camera
                    integration time.

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Argus-20

The Argus-20 Palette

                     Once you have installed the Argus-20 module, the Argus-20 Palette will be available
                     whenever you run Openlab.

                                                                                The link between the
The three buttons in the                                                        camera and the video
top panel control the                                                           display. At present, there
options that appear in                                                          are no additional
the middle panel                                                                processes or effects being
                                                                                applied.
      Processing
      operation

      Contrast                                                                   Use the middle panel to set
      enhancement                                                                up the parameters for
                                                                                 image processing. The
      Post-processing                                                            options vary according to
      operation                                                                  the icon and process/effect
                                                                                 selected.

Switches between
                                                                                  Adjusts which bit range of the
processed and raw
                                                                                  16-bit image is displayed
video
                                                  Stops/starts
                                                  processing

                    Transfers the current, processed
                    image to Openlab as a new layer

                                                                                                Argus-20    5
OPENLAB

      Using Openlab to Control the Argus-20

                     This section describes how to use the Argus-20 palette to control the Argus-20
                     computer. Read it for a step-by-step summary of the actions that you need to take.
                     Refer to the relevant, separate sections for comprehensive information on all the
                     available processes, contrast enhancement and post-processing options, and the valid
                     parameters that you can set for each.

                     Before you start, make sure that you have set up the Argus-20 Preferences, and that
                     you have also set up OpenlabÕs Video Manager for whatever camera is attached to the
                     Argus-20 computer.

                1.   Click on the Process icon.

                2.   Select the required process from the pop-up menu, and set up the appropriate
                     parameters. See page 10 for further details about processes.

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Argus-20

3.   If you want to apply contrast enhancement, click on the contrast enhancement icon.

4.   Select the required look-up table (LUT) from the pop-up menu, and set up the
     appropriate parameters. This operation will be carried out after any process has been
     applied. See page 17 for further details about LUT options.

5.   If you want to apply any post-processing, click on the Filter icon. This operation will be
     carried out after any process or LUT has been applied.

6.   Select the required filter from the pop-up menu, and set up the appropriate
     parameters. See page 23 for further details about Filter options.

                                                                                   Argus-20    7
OPENLAB

               7.   Click on the Start/Stop icon to carry out the operations. You should now be able to
                    see the real-time, processed video on your screen.

                    Notice how much information you can get from the Argus-20 palette. The top panel
                    shows you what type of operations are being carried out on the video image as it is
                    displayed on your screen. In the example below, the line now goes through all three
                    icons which means that a process, an LUT and a filter are being applied to the real-
                    time screen display. As the process icon is selected, we can see that the process is
                    averaging. Just click on the other icons to see which LUT and Filter are being applied.
                    Note also that the Start/Stop icon has changed and that there is an extra icon (circling
                    arrows) to show that the video data is currently being processed.

                                                                    Line indicates that
                                                                    process, LUT and filter are
                                                                    being/will be applied

                                                                    Extra features for
                                                                    cameras that support
                                                                    frame integration

                         Start icon       Circling arrows
                         has changed      indicate that the
                         to Stop icon     Argus-20 is active

                    The Integrate for section on the palette is not a standard feature. It is only displayed
                    if the camera (selected in the Preferences) supports frame integration. If it does, you
                    will be able to enter the time over which frames are to be integrated.

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Argus-20

8.     If you want to compare the processed image with the raw image, click on the video
       icon.

9.     If you want to select a different bit range, use the arrows to adjust the range to the
       required value.

10.    The processing operations will continue either for the time specified in the process
       parameters or until you stop them by clicking on the Start/Stop icon. If you want to
       change the process parameters, or any of the processes, always stop the current
       processing first. (Although you can change some of the parameters interactively, this
       can slow performance.)

11.    When you are satisfied with the effect of the processing operations, click on the
       Camera icon to transfer the current, processed image to Openlab as a new layer.

      Note: When you capture an image from the Argus-20 palette, the image data is
      transferred digitally from the Argus-20 computer to the Macintosh (via the data cable).
      The resulting image is high quality, but the process may be slow. You can also capture
      the image using the standard video capture icon in OpenlabÕs Document window. This
      uses the video channel and captures the exact image quickly, but you may lose some
      of the quality.

                                                                                     Argus-20    9
OPENLAB

       Processes

                   The following processes may be applied in real-time to the video signal:

                   Average

                   This process averages frames. It provides increased signal to noise for dynamic as
                   well as static images. You need to specify the number of frames over which the
                   averaging is to take place. This value must be a power of 2. Averaging will continue
                   until you click on the Stop icon to stop it or on the Camera icon to transfer the current,
                   processed image to Openlab.

                   Accumulation

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Argus-20

This process accumulates frames. It improves the quality (signal to noise ratio) of low
light or noisy images. You need to specify the number of frames over which the
accumulation is to take place. Check the Clear Memory First box if you want to reset
the memory prior to accumulation. Leave it unchecked, if you want Openlab to
continue accumulation from where it last stopped.

You may notice that the brightness of the live display changes during the
accumulation. This is because the software changes the bit shift values automatically.

Subtraction

This process subtracts input images from the stored image. You need to specify the
number of frames over which subtraction is to take place. Check the Clear Memory
First box if you want to reset the memory prior to subtraction. Leave it unchecked, if
you want Openlab to continue subtraction from where it last stopped.

You may notice that the brightness of the live display changes during the subtraction.
This is because the software changes the bit shift values automatically.

Background Subtraction

This process carries out background subtraction on an averaged image in real-time. It
eliminates background artefacts, such as dirt or uneven illumination, from each video
frame. There are two steps to setting up the process.

                                                                             Argus-20 11
OPENLAB

                1.   First you need to set the background image, which is normally accumulated over a
                     number of frames. Specify the accumulation value and then click in the Set
                     Background button.

                2.   Now specify the number of frames over which the main image is to be averaged. This
                     is normally the same as the Acc. value for the background subtraction. Use the Offset
                     value to control how bright or how dark the final image will be.

                     When you run this process, Openlab averages for the number of frames, subtracts the
                     background image, applies any offset adjustment and displays the resulting image.

                     Background Subtraction with Accumulation

                     This process carries out background subtraction on an accumulated image in real-
                     time. It improves image quality and enables quantitative analysis by subtracting dark
                     current or background fluorescence. There are two steps to setting up the process.

                1.   First you need to set the background image, which is normally accumulated over a
                     number of frames. Specify the accumulation value and then click in the Set
                     Background button.

                2.   Now specify the number of frames over which the main image is to be accumulated.
                     This is normally the same as the Acc. value for the background subtraction. Check the
                     Clear Memory First box if you want to reset the memory each time you run the
                     process.
                     When you run this process, Openlab accumulates for the number of frames, subtracts
                     the background image, and displays the resulting image.

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     Layer

     This process carries out background subtraction and overlays an averaged image on
     the background. There are two steps to setting up the process.

1.   First you need to set the background image, which is normally accumulated over a
     number of frames. Specify the accumulation value and then click in the Set
     Background button.

2.   Now specify the number of frames over which the main image is to be averaged. Use
     the Offset value to control how bright or how dark the final image will be.

     When you run this process, Openlab averages for the number of frames, overlays the
     current image on the background image, applies any offset adjustment and displays
     the resulting image.

     Sequential Subtraction

     This process carries out sequential subtraction on a sequence of images. It reveals
     only those objects which have moved or changed intensity by subtracting the previous
     frame from each incoming frame.

                                                                              Argus-20 13
OPENLAB

                You need to specify the subtraction interval. For example, if you specify an interval of
                2, the real-time display would be the result of the sequential subtraction as illustrated
                below:

                  1      2       3      4       5      6       7      8       9

                        3-1            5-3            7-5            9-7          Real-time image

                Extract Transients

                This process averages over a number of frames and extracts transient events. It
                reveals only those objects which have rapidly moved or changed intensity. The
                background changes slowly, as real-time averaged images are subtracted from each
                incoming frame.

                You need to select the value for averaging.

                Note: You cannot apply contrast enhancement or switch to raw video while the extract
                transients process is running.

                Mask

                This process applies a kernel filter to the image. It carries out edge extraction of the
                image, shadow enhancement and noise elimination. Select the appropriate filter from
                the Mask pop-up menu.

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Argus-20

Note: All masks are applied after the image has been processed. The resultant
display is therefore not a live, real-time image.

Trace

This process is useful if you want to trace the movement of an object. It compares
video images consecutively, at a given interval, and extracts their differences.

You set the interval at which frames will be sampled, by using the arrows to adjust the
value in the Interval box.

If you want to set a limit on the number of times the process will complete, check the
Stop automatically after box and use the arrows to specify a number in the
executions box. Otherwise, the process will continue until you stop it.

                                                                             Argus-20 15
OPENLAB

                Minimum Trace

                This process is useful if you want to trace the movement of a dark object on a bright
                background. It samples frames at certain intervals and then compares them, pixel by
                pixel. If it finds a pixel which is darker in the new image, it uses it to replace the
                corresponding pixel in the current image. Otherwise, it leaves the old image
                unchanged.

                You can set the interval at which frames will be sampled, by using the arrows to adjust
                the value in the Interval box.

                If you want to set a limit on the number of times the process will complete, check the
                Stop automatically after box and use the arrows to specify a number in the
                executions box. Otherwise, the process will continue until you stop it.

                Maximum Trace

                This process is useful if you want to trace the movement of a bright object on a dark
                background. It samples frames at certain intervals and then compares them, pixel by
                pixel. If it finds a pixel which is brighter in the new image, it uses it to replace the
                corresponding pixel in the current image. Otherwise, it leaves the old image
                unchanged.

16   Argus-20
Argus-20

     You can set the interval at which frames will be sampled, by using the arrows to adjust
     the value in the Interval box.

     If you want to set a limit on the number of times the process will complete, check the
     Stop automatically after box and use the arrows to specify a number in the
     executions box. Otherwise, the process will continue until you stop it.

     Photon Counting

     This process is for use with the Hamamatsu Image Intensifier (see separate document
     for instructions on using the Openlab Image Intensifier module).

     Photon Counting allows you to count events in an image. There are two steps to
     setting up the process.

1.   First you need to set the discriminator Level which defines what counts as an event.
     Anything above the level, counts as an event.

     Note: To see a picture of events from the video signal, click on the Show level button.

2.   Now specify the time over which photons will be counted. The time interval may be
     expressed in terms of Frames, Seconds, Minutes or Hours, by selecting the
     appropriate option from the pop-up menu. Check the Clear Memory First box if you
     want to reset the image memory each time you run the process.

     When you run this process, the Argus-20 looks at each pixel in the incoming video
     signal and decides whether it is an event or not. If it is, it adds one grey level to the
     corresponding pixel in the image memory. If it is not, it ignores it.

                                                                                      Argus-20 17
OPENLAB

       Contrast Enhancement

                    Various LUTs may be applied in real-time to the video output. These LUTs only affect
                    the way that you see the image on the screen; they do not change the underlying 16
                    bit data until you transfer the image to the Macintosh.

                    The act of transferring the image applies the contrast enhancement, which always
                    produces an 8 bit result. This means that if you transfer the contrast enhanced image
                    digitally to the Macintosh, you will get an 8 bit grey image, rather than a 16 bit grey
                    image.

                   Positive

                    This is the default LUT; it does not change the image at all.

                   Negative

                    This LUT inverts the image.

                   Slice LUTs

                    The four Slice LUTs allow you to specify a range of values. You need to set up a start
                    value and an end value for the range. Different effects will be applied to pixels that fall

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within, and outside of, the range, depending upon which LUT you have chosen. Slice
LUTs are useful if you want to pick out a range of intensities.

                                     Anything between the
                                     specified range is white.

                                     Anything outside the
                                     specified range is black.

                                     Anything between the
                                     specified range is black.

                                     Anything outside the
                                     specified range is white.

                                     Anything between the
                                     specified range is white.

                                     Anything outside the
                                     specified range is left
                                     alone.

                                     Anything between the
                                     specified range is white.

                                     Anything outside the
                                     specified range is inverted
                                     from the original.

                                                                         Argus-20 19
OPENLAB

                Stretch LUTs

                The four Stretch LUTs allow you to specify a range of values. Pixels that fall within the
                range will be stretched from black to white. This allows you to improve the contrast in
                the image.

                You need to set up a start value and an end value for the range. Different actions will
                be applied to pixels that fall within, and outside of, the range, depending upon which
                LUT you have chosen.

                                                       Anything below the minimum value is
                                                       black.

                                                       Anything above the maximum value is
                                                       white.

                                                       Anything within the range is stretched
                                                       from black to white

                                                        Anything below the minimum value is
                                                        white.

                                                        Anything above the maximum value is
                                                        black.

                                                        Anything within the range is stretched
                                                        from white to black and inverted over the
                                                        range.

                                                       Anything below the minimum value is
                                                       black.

                                                       Anything above the maximum value is
                                                       black.

                                                       Anything within the range is stretched
                                                       from black to black.

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Argus-20

                                      Anything below the minimum value is
                                      black.

                                      Anything above the maximum value is
                                      black.

                                      Anything within the range is stretched
                                      from black to black and inverted.

Gamma LUTs

The Gamma LUTs allow you to apply one of four different types of gamma correction
to the image. Refer to the Argus-20 manual for a detailed description of each of the
gamma corrections.

Select the appropriate value for the gamma correction.

                                                                          Argus-20 21
OPENLAB

                Wing LUT

                The Wing LUT splits the range into three sections:
                n    the first section is scaled white to black

                n    the second section is black

                n    the third section is scaled black to white.

                You need to select a value to control the width of the second section.

                                                         Select a value to control the width of the
                                                         middle section.

                                                         Anything to the left of the section is scaled
                                                         white to black: anything to the right is
                                                         scaled black to white.

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Argus-20

Post-Processing

             The following filters may be applied in real-time to the processed, live image.

              Filter                          Effect
              Edge                            Extracts edges, eliminates noise and sharpens the
                                              image to make it clearer.
              Sharpen                         Sharpens the image.
              Smooth                          Smoothes the image.
              Divide                          Displays an image showing the intensity ratio of two
                                              different images. You need to set a background image
                                              and a ratio range. See separate section.
              Real-Time Mask                  Not yet available

             With the exception of the Divide filter, there are no parameters to enter. The filter is
             simply applied to the video display.

             Note: The filtered image is not transferred digitally if you capture the image from the
             Argus-20 palette. If you want to capture the image with the filter applied, use the
             camera icon in the Document window (in the Openlab Toolbar).

                                                                                            Argus-20 23
OPENLAB

                        Divide

                        There are two steps to setting up the process.

                 1.     First you need to set a Ratio Range. Use the arrows to set the required value.

                 2.     Now display the image which is to divide incoming images and click on the Set
                        Background button. Processed images will now be displayed divided by the
                        background image.

       Hints and Tips

                        You may find the following hints and tips useful when you are running the Argus-20
                        module:

                        Unexpected results

                        n    If you get unexpected results, the Argus-20 and the Macintosh may not be in
                             sync, with each other. Check that the Preferences have been set up correctly.

                        n    If the image is completely black, check that the camera is switched on. If it is, try
                             adjusting the bit shift value downwards to try and locate a more sensitive part of
                             the image.

                        n    If the image is completely white, try adjusting the bit shift value upwards to try
                             and locate a less sensitive part of the image.

                        n    Some processes, such as Accumulation and Subtraction, display a progress bar
                             on the Argus-20 palette. If the progress bar does not appear on your palette, you
                             are running an Argus-20 Firmware version which does not support it. You can
                             easily obtain an update. Contact your Argus-20 supplier and ask for an update to
                             Firmware version 2.460 or later.

24   Argus-20
Argus-20

Adjusting parameters

n   For some processes, it may take Openlab a while to carry out adjustments to
    parameters if the process is still running. If you stop the process before you
    adjust the parameters on the Argus-20 palette, you will allow Openlab to carry out
    the adjustment much more quickly.

n   When you specify the time in frames, the actual timing depends upon the type of
    system that you are using. For example, PAL runs at 25 frames per second;
    NTSC at 30 frames per second.

Contrast Enhancement

n   When you apply contrast enhancement to a real-time image, it always produces
    an 8 bit result. This means that if you subsequently transfer that image to the
    Macintosh, you will only get an 8 bit image and not a 16 bit image.

n   When you transfer a contrast enhanced image to the Macintosh, the Argus-20
    actually applies that contrast enhancement to the image. The following example
    illustrates what happens to the screen display and the image in the Argus-20; first
    when you apply a negative LUT and then when you transfer it to the Macintosh.

                                                                           Argus-20 25
OPENLAB

       The Argus-20 and Automator tasks

                    If you have the Automator module and the Argus-20 module, you will be able to use
                    the Argus 20 tasks in your automation. The tasks will appear in either the Argus-20
                    Imaging or the Argus-20 Processing Task List in the Automator Window.

                    This section describes the Argus-20 tasks. Refer to the Automator Reference Manual
                    for further details about creating and running automations.

                    Argus-20 Imaging Tasks

26   Argus-20
Argus-20

The Argus-20 imaging tasks allow you to automate those tasks that you would control
manually from the icons at the bottom of the Argus-20 palette, as illustrated below.

                         Stops/starts
                         processing

Switches display                             Indicates that image
between raw and                              is being processed
processed image

                     Transfers processed
                     image to Macintosh

Start Imaging

This task allows you to start the imaging process.
There are no set up parameters.

Stop Imaging

This task allows you to stop the imaging process.
There are no set up parameters.

                                                                          Argus-20 27
OPENLAB

                Transfer Image

                This task allows you to transfer a processed image from the Argus-20 to the
                Macintosh as a new layer. You can specify a name for the new layer.

                                                                           Enter an expression to
                                                                           create a name for the
                                                                           transferred layer

28   Argus-20
Argus-20

Get Imaging Status

This task allows you to query the imaging status.
n    If processing is taking place, the status will be 1.

n    If the Argus-20 is idle, the status will be 0.

Openlab puts the returned status value into a variable. You use the Setup dialogue to
specify which variable will be used for the status value.

                                                            Select a variable
                                                            from the pop-up list

Set Image Display

This task allows you to set the image display to either processed video or raw video.

                                                             Click on appropriate
                                                             button

                                                                           Argus-20 29
OPENLAB

                Argus-20 Processing Tasks

                The Argus-20 processing tasks allow you to automate any of the Argus-20 processes.

30   Argus-20
Argus-20

Average

This task allows you to average frames. You need to specify the number of frames
over which the averaging is to take place. This value must be a power of 2.

When you use this task within your automation, remember that averaging will continue
until you stop it or until you transfer the processed image to Openlab.

                                                          Enter an expression
                                                          for the number of
                                                          frames

                                                                        Argus-20 31
OPENLAB

                Accumulation

                This task allows you to accumulate frames. You need to specify the number of frames
                over which the accumulation is to take place. Check the Clear Memory First box if
                you want to reset the imaging memory prior to accumulation. Leave it unchecked, if
                you want Openlab to continue accumulation from where it last stopped.

                                                                            Enter an expression
                                                                            for the number of
                                                                            frames

                                                                            Check this box to
                                                                            clear memory before
                                                                            accumulation starts

                Subtraction

                This task allows you to subtracts frames. You need to specify the number of frames
                over which subtraction is to take place. Check the Clear Memory First box if you
                want to reset the imaging memory prior to subtraction. Leave it unchecked, if you
                want Openlab to continue subtraction from where it last stopped.

                                                                            Enter an expression
                                                                            for the number of
                                                                            frames

                                                                            Check this box to
                                                                            clear memory before
                                                                            subtraction starts

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Argus-20

Background Subtraction

This task carries out background subtraction on an averaged image in real-time. You
need to specify:
n   The number of frames over which the main image is to be averaged

n   The Offset value to control how bright or how dark the final image will be.

Before you use this task in an automation, you will need to use the Capture
Background task to capture the background image for subtraction.

                                                             Enter an expression
                                                             for the number of
                                                             frames

                                                             Enter an expression
                                                             for the offset value

                                                                           Argus-20 33
OPENLAB

                Background Subtraction with Accumulation

                This task carries out background subtraction on an accumulated image in real-time.
                You need to specify the number of frames over which the main image is to be
                accumulated, and should also check the Clear Memory First box if you want to reset
                the imaging memory before the automation runs the process.

                Before you use this task in an automation, you will need to use the Capture
                Background task to capture the background image for subtraction.

                                                                              Enter an expression
                                                                              for the number of
                                                                              frames

                                                                              Check this box to
                                                                              clear memory before
                                                                              process starts

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Argus-20

Capture Background

This task allows you to capture a background image for use with other processes,
such as background subtraction. You need to specify the number of frames over
which the background image will be accumulated before it is captured.

                                                             Enter an expression
                                                             for the number of
                                                             frames

Sequential Subtraction

This task carries out sequential subtraction on a sequence of images. You need to
specify the subtraction interval.

                                                            Enter an expression
                                                            for the subtraction
                                                            interval

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OPENLAB

                Extract Transients

                This task averages over a number of frames and extracts transient events. You need
                to specify the number of frames for averaging.

                                                                               Enter an expression
                                                                               for the number of
                                                                               frames

                Apply Mask

                This task applies a kernel filter to the image. You need to select the appropriate mask
                from the pop-up menu.

                                                                    Select a mask from
                                                                    the pop-up menu

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Argus-20

Trace

This task allows you to trace images. You need to set the interval at which frames will
be compared. If you want to set a limit on the number of times the process will
complete, check the Stop automatically after box and specify the number of
executions.

                                                             Enter an expression
                                                             for the frame interval

                                                             Check this box and
                                                             enter an expression
                                                             for the number of
                                                             executions, if you do
                                                             not want the trace to
                                                             continue indefinitely

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OPENLAB

                Maximum Trace

                This task selects frames at certain intervals and then compares them, pixel by pixel. It
                leaves the old image unchanged, unless it finds a pixel which is brighter in the new
                image, in which case it replaces it. The process is useful if you want to trace the
                movement of a bright object on a dark background.

                You need to set the interval at which frames will be compared. If you want to set a
                limit on the number of times the process will complete, check the Stop automatically
                after box and specify the number of executions.

                                                                               Enter an expression
                                                                               for the frame interval

                                                                               Check this box and
                                                                               enter an expression
                                                                               for the number of
                                                                               executions, if you do
                                                                               not want the trace to
                                                                               continue indefinitely

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Argus-20

Minimum Trace

This task selects frames at certain intervals and then compares them, pixel by pixel. It
leaves the old image unchanged, unless it finds a pixel which is darker in the new
image, in which case it replaces it. The process is useful if you want to trace the
movement of a dark object on a bright background.

You need to set the interval at which frames will be compared. If you want to set a
limit on the number of times the process will complete, check the Stop automatically
after box and specify the number of executions.

                                                                Enter an expression
                                                                for the frame interval

                                                                Check this box and
                                                                enter an expression
                                                                for the number of
                                                                executions, if you do
                                                                not want the trace to
                                                                continue indefinitely

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OPENLAB

                Photon Counting

                This task allows you to count events in an image. You need to specify the time over
                which photons will be counted. You may also like to check the Clear Memory First
                box if you want to reset the imaging memory each time you run the process.

                Remember that, before you use this task in an automation, you will need to use the
                Set PC Discriminator Level task to define what counts as an event.

                                                                            Enter an expression
                                                                            for the time over
                                                                            which photons will be
                                                                            counted

                                                                             Use the pop-up menu
                                                                             to define the time
                                                                             interval as:

                                                                             Check this box to
                                                                             clear memory before
                                                                             process starts

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Argus-20

Set PC Discriminator Level

This task allows you to define what counts as an event for the Photon Counting task.
Anything above the level, counts as an event.

                                                              Enter an expression
                                                              for the discriminator
                                                              level

Set Integration

This task is only available if your camera supports frame integration. It allows you
specify the number of frames over which integration will take place.

                                                             Enter an expression to set
                                                             the integration period

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OPENLAB

                Layer

                This task allows you to carry out background subtraction and overlay an averaged
                image on the background. You need to specify the number of frames over which the
                main image is to be averaged. Use the Offset value to control how bright or how dark
                the final image will be

                Before you use this task in an automation, you will need to use the Capture
                Background task to capture the background image for subtraction.

                                                                         Enter an expression for the
                                                                         number of frames over which
                                                                         the image is to be averaged

                                                                         Enter an offset value, if
                                                                         required

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Argus-20

Automation - Hints and Tips

              n   If you are using any of the tasks which apply background subtraction, remember
                  that you must capture the background first. This is a separate task in the
                  Automator.

              n   If you are using any of the tasks which accumulate or subtract information, you
                  need to check the Clear Memory First box if you want to reset the imaging
                  memory before processing starts.

              n   There is a pattern to the flow of tasks within an Argus-20 automation.
                  1. Specify which imaging process you want to carry out.
                  2. Define any further setup tasks, such as capturing a background.
                  3. Some imaging processes need to continue for a certain length of time before
                     the image is ready for transfer. For example, photon counting waits until the
                     number of counts reaches the preset threshold (discriminator level). Set up a
                     loop for such tasks which includes the Get Imaging Status task. This
                     ensures that the automation will wait until the task has finished before it tries
                     to carry out another task, such as Image Transfer.
                  4. Start the imaging process.
                  5. Transfer the processed image as a new layer to Openlab.

An Example Automation

              The following example counts photons emitted from a sample, continuing until the
              maximum count reaches a preset threshold. The image is captured from the Argus-20
              at regular intervals, defined by the testPeriod seconds variable.

              You must have an empty image document open for this automation to work. The
              document should have an ROI set to the area that you want to scan for photon levels.

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OPENLAB

                Setting up the automation

                The automation is set up as follows:
                n    First, you need to set up some variables. There are three Variable tasks which
                     set the start values for the image number (1) and the two photon counts (both 0).
                     The image number variable will be used to ensure that each processed,
                     transferred layer has a unique name. (See the Transfer Image task.) The two
                     count variables will be used to compare how the count has increased for each
                     new layer that is captured. (See the Tell task.)

                n    Next, you need to get some information from the user so that the automation
                     knows how many photons it is to count, and how often it should capture the
                     image and transfer it from the Argus-20 computer to the Macintosh.

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Argus-20

    The first Input task prompts the user for a target count and puts the answer into a
    variable called ÒwantedCountÓ.

    The second Input task prompts the user for the period between tests and puts the
    answer into a variable called ÒtestPeriodÓ.

n   The Target Image Window task defines the target image window in Openlab on
    the Macintosh. Make sure that you select the empty image document on which
    you have already defined an ROI set to the area that you want to scan for photon
    levels.

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OPENLAB

                n   The Count Measurements task counts the number of measurements in the
                    Measurements ROI table and puts the results of the count into a variable called
                    ÒinitialMeasuresÓ.

                n   The Set PC discriminator level task sets the level at which events will be counted.

                n   The Stop Imaging task ensures that the Argus-20 is idle before photon counting
                    starts.

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Argus-20

n   The first Photon Counting task clears the memory and specifies the count period
    which was provided by the user and stored in the ÒtestPeriodÓ variable.

n   The first If task checks whether the current count (ÒthisCountÓ) is less than the
    target count specified by the user (and stored in the ÒwantedCountÓ variable).

    If it is, the automation continues with the remaining tasks. If it is not, it exits.

n   The Switch to preview View layer task displays the Video Preview in OpenlabÕs
    Image Document window.

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OPENLAB

                n   The Start Imaging task starts the photon counting process.

                n   The Get Imaging Status task checks whether the photon counting process is
                    currently active, and puts the returned status value into a variable called
                    ÒimageStatusÓ.

                n   The second If task then checks the imageStatus value. If it is Ò1Ó, then the photon
                    counting process is still active, and the automation will continue checking the
                    status until it returns a value of Ò0Ó, which indicates that the photon counting
                    process has finished.

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Argus-20

n   The Transfer Image task transfers the processed image to the Macintosh as a
    new layer. It includes the ÒimageNoÓ variable in the layer name to uniquely
    identify the layer.

n   The second View Layer task displays the layer that has just been transferred in
    OpenlabÕs image document window.

n   The Capture one measurement task captures the layerÕs measurements.

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OPENLAB

                n   The Extract Measurement task looks at the ROI measurement table and extracts
                    the maximum grey level intensity value (ÒMaxÓ) for the current layer
                    (initialMeasures+imageNo). It puts the result into the variable called ÒthisCountÓ.

                n   The Tell task allows you to track current status by displaying various pieces of
                    information in a trace message. The Tell expression tells you how long photon
                    counting has been going on for, how levels have increased during this period,
                    what the current photon level is and how many seconds it is likely to be until the
                    automation has completed.

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Argus-20

n   The first of the two Variable tasks in the If loop (lastCount=thisCount) sets the
    lastCount variable equal to thisCount, so that the automation will be able to work
    out the increase in levels for the Tell task, on the next iteration of the If loop.

n   The second Variable task (Inc frame count) increments the image number by 1,
    so that the next time that the automation transfers an image in the If loop, it will
    have a unique identifier in the Openlab Layer Manager palette.

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OPENLAB

                n   The Photon Counting task continues the photon counting process (which stopped
                    automatically when the automation transferred the layer from the Argus-20 to the
                    Macintosh). Note that the Clear memory first box is now blank, because you do
                    not want to reset the levels to 0.

                n   The automation now returns to the first If task to check whether the current count
                    (ÒthisCountÓ) is less than the target count specified by the user (and stored in the
                    ÒwantedCountÓ variable). If it is less, it repeats the If loop. If it is equal to or
                    greater, the automation exits.

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