iQ Release Notes

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					                                                                       Andor Technology
                                                                        7 Millennium Way
                                                                 Springvale Business Park,
                                                                       Belfast, BT12 7AL,
                                                                  NORTHERN IRELAND

                                                                    Tel: +44 28 9023 7126
                                                                    Fax: +44 28 9031 0792

GENERAL GUIDANCE:


                                                                                   nd
     If 2 Andor Neo cameras are attached to the system, you must not start up a 2
                                 st
     instance of iQ while the 1 instance of iQ is currently acquiring images from Neo. This
     will disrupt the acquisition and may cause the system to crash. This is a known issue
     and we are currently working to address it.

     Windows 7 requires the user account to have administrator privileges in order to run
     Configuration Manager.

     On Windows 7, working with large data sets may cause Windows to declare that iQ is
     "Not Responding". iQ is still processing and is only temporarily unresponsive. User
     Interface responsiveness in Windows 7 is a priority in upcoming releases.

     From iQ 2.4 onwards, driver files for Andor USB camera, iXon CCI PCI cards, and
     Andor Laser Combiner are no longer located in the “Common Files” directory. They
     are now organised in a “Drivers” subdirectory inside Common Files.

     Andor iQ 2.2 and onwards does not support Andor FRAPPA devices with firmware
     earlier than 3.5.10. If your device has earlier firmware please contact support for
     assistance on getting a free firmware update.

     http://www.andor.com/contact_us/support_request/
Andor iQ Release Notes


Andor iQ 2.4.4
September 2011

Introduction

This incremental release of iQ provides a critical bug fix.



Bug Fixes

        Fixed a bug where a long delay (5-20 seconds) might occur when acquiring a Snap or
        when starting a protocol.




Andor iQ 2.4.3
September 2011

Introduction

This incremental release delivers an update for Andor Neo cameras that allows 2 Neos to
acquire simultaneously using 2 instances of iQ on a single workstation.
This release also adds support for the F0S variant of the Andor AMH device.
2 bug fixes are also provided.

New Features

        Two Andor Neo cameras can acquire simultaneously on a single workstation running
        2 instances of iQ. To enable this feature, please download the latest
        BitFlowInstallerForiQ from http://www.andor.com
        The F0S variant of the Andor AMH device is now supported



Bug Fixes

        Fixed a bug where the default resolution for an ASI XYZ stage would be 1.0 instead
        of 0.1.
        Fixed a bug where “Stage failed to move” events occurred when running an XY scan.
        This was due to the “stage tolerance” setting not being correctly applied to stage
        movements.
Andor iQ Release Notes


Andor iQ 2.4.2
September 2011

Introduction

This incremental release addresses an issue with Olympus BX-series microscopes in iQ2.



Bug Fixes

       Fixed a bug where iQ could not connect to Olympus BX microscopes.
Andor iQ Release Notes


Andor iQ 2.4.1
August 2011

Introduction

This incremental release provides some important bug fixes for iQ2.



Bug Fixes

        Fixed a problem where iQ would appear unresponsive for up to a minute when
        viewing a dataset with a large number of frames and at least one event (FRAPPA
        event, keyboard input event etc).
        Fixed a bug where AutoFocus in a MultiField XY scan might only properly focus for
        the first field.
        Fixed a bug where attempting to edit filter wheel labels and colours for a Yokogawa
        CSU caused error messages to appear.
        Corrected a typo for Yokogawa CSU – “Statuss” is now “Status”.
        Fixed a bug in the iQ installer where the “Back” button does not follow the same order
        of installation steps as the “Next” button.
Andor iQ Release Notes


Andor iQ 2.4
July 2011

Introduction

This new release of iQ delivers support for Windows 7 32-bit and contains a number of bug
fixes, with a focus on bugs reported through Andor support.
Lumencor is now supported and can be controlled using the Andor Generic Shutter interface
– see appendix 5.21 of the iQ2 user guide for details.

New Features

       Windows 7 32-bit is now supported.
       Andor Mosaic now has a “White Mask” setting that turns all mirrors on, to aid
       alignment/setup.
       The default temperature for an Andor Clara camera is now -45.
       Images with more than one Time dimension can now be viewed in iQ as a single time
       series using the “Flatten Time” control in the Navigator Toolbar.
       A new Auto-Focus control panel has been added to the Z Scan wizard.
       Negative Z stacks (top to bottom) can be executed.
       The installation of Python IDE no longer requires iQOpenSource as a pre-requisite.
       This change gets rid of the warning that appears when installing iQ; and allows user
       to install iQ first and iQOpenSource later.
       Configuration Manager lists devices in alphabetical order.
       iQ now installs Desktop and Start menu shortcuts for all users
       iQ will now warn you if you choose to delete images that have dependants (e.g.
       constructor images created by the Dual Image Disk plug-in).
       The Dual Image Disk plug-in has been enhanced:
            o Local copy of source image is now deleted after construction.
            o Option to skip copy if the remote disk is the same as the local.
            o Ability to merge images that differ by +/- 1 frames in length.


Bug Fixes

       Andor Laser Combiner is now compatible with version 6.10 of the InstaCal software for
       DAC card.
       Fixed a compatibility issue between iQ and the Olympus software for BX microscopes.
       Yokogawa CSU – the transition delay after a filter wheel move is now proportional to the
       wheel speed. This fixes a problem where “smeared” frames might be acquired after
       changing channel.
       Fixed a bug where opening the Field Split tool while the camera was Live would freeze iQ.
       Fixed a bug where a montage including multiple XY or Time positions would be stitched
       incorrectly if the “Pixel Matching” option was used.
       Fixed a bug where enabling “Frame Transfer” would change the camera exposure time to
       0ms.
       Fixed a potential crash if user clicked the Live/Idle button rapidly.
       Fixed a crash when saving an image acquired by iQ 1.10 as a Multi-TIFF.
       Fixed a bug where “Move XY” in a protocol would move the Z stage device to the wrong Z
       position.
       Fixed a bug where Auto Save tries to write to a file path containing invalid characters
       Fixed a bug where Frame Transfer could remain enabled in a protocol that used Snap –
       Frame.
       Andor Generic Shutter memory leak fixed.
Andor iQ Release Notes

      Fixed access violation errors when disconnecting from the Mosaic device on a Windows 7
      system.
      Fixed hotkeys (e.g. F1) not working after running a protocol.
      Configuration Manager no longer crashes when launched in Windows 7.
      Fixed a crash when saving a single image as multi-TIF.
      Fixed a bug where starting to create a new XY scan then cancelling would cause the
      current protocol to fail to move the XY stage.
      Fixed a bug where hard drive space was still being used after deleting images in iQ.
      Fixed the protocol Repeat Interval becoming stuck at a huge value (e.g. 61 hours).
      If saving an image and using the Dimension Split save option, the image details text file is
      now saved along with the tif image.
      Fixed errors appearing when attempting to use Strip View tool for larger images.
      The ClearView plug-in no longer writes temporary files to the Windows desktop.
      Fixed a bug where binning options for iXon disappeared when an Andor Neo camera was
      also connected.
      DG4 device now shows the correct connection state.
      Fixed a bug where a protocol including a Multi Field and Montage XY scan would become
      unusable if the XY scan was edited and reduced to only one field.
      Added a warning to the user when attempting to delete images from the image disk which
      have dependent images that are also going to be deleted.
      Images constructed by the Dual Image Disk tool now retain all of the image details (e.g.
      protocol and channel settings) that were stored in the original image.
      "FRAPPA on mouse up" no longer applies to ROIs drawn with the red Background
      classification. This prevents FRAPing from occurring by accident when using a
      Background ROI e.g. in the manual calibration wizard.
      Fixed a bug where a channel could become corrupted, causing the error "- <channel
      name> is not a valid floating point value" to appear.
      Fixed a bug in the 1.10.5 executable where the Device Setup window could become stuck
      at the top left of the screen.
      “DSD RAW Processor” is now available in the “Process” menu.
      The XY Scan wizard now forbids you from creating a Montage scan with only one field.
      The Dual Image Disk plug-in now automatically refreshes both image lists after a
      Construct operation.
      “External Start” has been enabled for the Andor Neo camera.
      Images created by the DSD RAW Processor can now be processed by the Montage tool
      Fixed a bug in a master/slave setup where the "slave" instance of iQ could end its protocol
      with an extra blank frame.
      The iQ installer now grants write/modify permissions to “Everyone” on the Kinetic Imaging
      configuration folder. This removes the need for an admin user to do this manually; and
      stops non-admin users from seeing a permissions warning when starting iQ
      Fixed a crash when using the Dual Image Disk in Windows 7 when you press “Remote
      image disk 1”.
      Fixed a bug where the image did not entirely fit in the display after using "Auto Zoom"
      Fixed a bug where the Image List window would lose buttons after being resized to a
      small size.
      Image Zoom now defaults to 100% when starting iQ instead of 1000%.
      Image Contrast - the "Map Options" window has been resized so that the Submit/Cancel
      buttons are fully visible.
      Removed "Button1" from the Kinetic Dummy Camera controls.
      Removed the option to disable baseline clamp on an Andor Neo camera.
      It’s now possible to drag-and-drop "Move Scan Z" in the protocol tree.
      The default size of the Field Split window has been increased.
      Image Contrast – the Confirm and Cancel buttons are correctly hidden when closing the
      "Map Options" window.
Andor iQ Release Notes


Andor iQ 2.3.1
May 2011

Introduction

This is an incremental release that addresses some issues in Andor iQ 2.

New Features

        iQ’s start-up time for systems with multiple cameras has been improved. iQ is now up
        to 10 seconds faster when initialising multiple Andor cameras.
        The “Error Handling” tab of the camera settings now has an option to display “FIFO
        Usage”. If the user is running intensive protocols with an Andor Clara, “FIFO Usage”
        will indicate if the protocol is approaching/exceeding the PC’s ability to pull image
        data from the Clara.

Bug Fixes

        Fixed a crash that could occur when running 2 instances of iQ; if the user started a
        protocol after deleting images from the image disk.
        Fixed a crash that could occur if a protocol contained more than 7 repeat loops.
        Fixed excessive memory usage for Andor cameras. This resolves a problem where iQ
        ran out of memory when 3 Andor cameras were connected.
        Widened the input field for “Timeout” of the Andor camera external trigger. Previously,
        only 4 digits were visible even if more digits were typed.
        Fixed a bug where a “setExposureTimeInSDK” error might appear when starting up
        iQ in a dual camera system.
        Fixed a bug in iQ 2.3 for systems with multiple cameras; where the name displayed
        for a camera might be the model/serial number of a different camera.
        Fixed a bug where error messages might appear if changing camera settings while
        the camera is running Live.
        If saving large datasets that include the “Montage” dimension, iQ no longer splits the
        image in the Montage dimension. The image is split by XY and Time first.
        Fixed a bug where montage images could not be stitched together after processing
        with the Image Math tool. This was due to the Image Math tool not copying image
        details from the input image to the output image.
        Fixed a bug where the Field Split tool did not copy image details from the source
        image to the resulting split images.
Andor iQ Release Notes


Andor iQ 2.3
March 2011

Introduction

This release sees the integration of the revolutionary Andor Neo sCMOS camera. This much
anticipated, highly innovative camera platform is a true scientific CMOS in every sense, Neo
has been conceptualised and specifically engineered to harness the full performance potential
of this new and exciting sensor technology. Unlike any CCD or CMOS camera to come
before, Neo is unique in its ability to simultaneously offer ultra-low noise, extremely fast frame
rates, wide dynamic range, high resolution and a large field of view.

New Features

        Andor Neo sCMOS integration.
        Olympus ZDC2 integrated.
            o NOTE: The Olympus IX2 or BX2 software supplied with your scope must
                be installed and the device configured for Andor iQ to connect.
        External Start trigger re-introduced to flexible protocol.
        Allow Z scans to move in the negative direction and choose the start point as
        the start or centre.
        Marzhauser Adapter: Added Baud Rate option to support newer LSTEP/Tango
        based units which have 57600 capabilities.
        Improved splitting of dimension when saving files.


Bug Fixes

        Fixed ZDC Range on Olympus not applied on connection.
        Fixed IX81 range selection - AF near and far limit were not being set correctly.
        Fixed PFS not working correctly on TE2000.
        Improved stability of ALC laser start-up.
        Fixed DG4 incorrectly showing as Connected when not connected.
        Fixed a problem with DSD systems where aborting a protocol would cause the
        “Imaging” dimension to be lost.
        Removed check for duplication of filter and wavelength names in AMH.
        Fixed unhandled error and crash when opening invalid (ImageJ) TIFF file.
        Fixed saved OME TIFF having the LUT inverted.
        Fixed filename name losing last character when saving Split Multi-Field TIFF.
        Fixed mapping option corrupted on TIFF save.
        Fixed spurious file created when cancelling "Save As" dialog for split multi-field
        image.
        Fixed saving of multiple TIFF files results in incorrect/blank file names.
        Fixed MM40 error when splitting TIFF into fields.
        Fixed TIFF file saving for large datasets.
        Fixed crash when saving images as 8 bit single TIFF.
        Removed prompt for multi image TIFF save for each file.
        Fixed dual camera issue where wrong camera settings displayed.
        Fixed infrequent timeout and channel mix-up with Snap Frame and iXon 897.
        Fixed DU885 not working with Snap Frame.
        Fixed 885 external trigger timeouts with Snap Frame.
        Fixed exposure time possibly having incorrect value in multi-channel stream mode.
        Fixed DSD background correction possibly having incorrect value in multi-channel
        protocol
        Fixed Hamamatsu camera cannot be used to generate Montage Images.
        Fixed pre amp gain setting incorrectly in Clara.
Andor iQ Release Notes

      Fixed timeout on Snap when shutter set to closed.
      Improved repeat interval timing.
      Added option to switch camera saturation check on/off. Off can speed up acquisition.
      Added option for camera error frames - blank frames or checkerboard.
      Fixed cannot drag and drop "Move Scan Z".
      Fixed tree errors when adding or modifying scans.
      Fixed Repeat interval changing to large times and cannot be changed.
      Fixed Format Converter problem when splitting RGB Images.
      Fixed templates - FRAPPA template caused crash when ran.
      Fixed floating point image mapping.
      Fixed channel LUT can get overwritten when using channel "Record" button.
      Fixed interactive FRAPPA during Z-stack protocol will not execute until end of Z
      stack.
      Fixed Line profile graph horizontal axis for larger sensors (limited to 1024 previously).
      Fixed Line profile Error messages if line profile open and user sets a line start and
      end the same.
      Improved responsiveness of Rolling Ball Filter.
      Allowed RGB split to be cancelled.
      Improved stability and error handling of 4D view and Fast MIP.
      Improved error messages for Imaris launcher when using virtual image disk (not
      supported).
      Added warning on failed Andor FRAPPA connection.
      Improved FRAP Analysis to allow a time period and its last interval to be extended
      past the end of a chart series.
      Improved channel saving so settings saved in case of crash.
      Fixed acquisition slowdown when using OnLine Chart in certain protocols.
Andor iQ Release Notes



Andor iQ 2.2.2
January 2011

Introduction

This is an incremental release that addresses some issues in Andor iQ 2.


Bug Fixes

        Fixes problem of some acquisition modes not working for iXon 885 cameras.
        Fixes a bug where clicking Live then Idle would overwrite the colour LUT of the
        currently displayed image.
        Fixes a bug where saving a large dataset fails if user chooses to split the output into
        one TIF file per XY field.



Andor iQ 2.2.1
January 2011

Introduction

This is an incremental release that addresses some issues in Andor iQ 2.2.


Bug Fixes

        Fixes acquisition slowdown when using the DSD system with long, multi-channel
        acquisitions.
        Fixes Trigger devices not registering correctly in Configuration Manager.
        Fixes Time Out for camera external trigger; iQ was not using Time Out values typed
        in by the user.

Andor iQ 2.2
December 2010

Introduction

Andor Technology proudly releases iQ 2.2. This release integrates the Revolution DSD
system into the advanced iQ 2 stream. The flexibility provided by iQ 2 facilitates faster
acquisition and more control over the Revolution DSD system. This release also improves
FRAPPA experimentation by providing multiple selection on regions, dual FRAP with any
region classification and extensive quantitative FRAP analysis.

New Features

        DSD integration and enhancements
           o Integrated Revolution DSD into iQ 2 - gives significant performance increase
               to the DSD system.
           o Adding saturation check to unprocessed Rev DSD images.
           o New DSD Filter turret sets supported as standard.
Andor iQ Release Notes

            o  Adding Fast Refresh to Andor Camera - maintains a fast refresh when live
               even with long exposures (simulates exposure).
           o Adding digital gain (only for Andor Clara).
           o Added Light Source Filter wheel into Revolution DSD Background Correction.
      FRAP Analysis and Enhancements
           o Added FRAP Analysis - allows quantitative analysis of FRAP experiments.
           o Added multi-region selection (Ctrl modifier to add individual regions, Shift
               modifier to select all regions of a particular class).
           o Added multi-region classification for FRAPPA (allows different FRAPPA
               devices to FRAP only specific types of regions).
      Fast Acquisition via Stream Mode
           o Added Snap Frame and Snap burst to allow option of synchronised
               (traditional) or very fast acquisitions.
           o Added support for external trigger in burst mode.
      Protocol Creation and Editing
           o Added protocol templates - allows easier construction of complicated
               experiments
           o Re-designed Repeat Channel edit dialog.
           o Revamped Z scan wizard - Adding direct editing of scan position and adding
               "move to" buttons.
           o Added Drag and Drop to protocol tree.
           o Revised Device Setup GUI layout.
      Automap Improvements
           o Added smoothing functionality to Automap - only updates mapping when
               counts changed by specified percentage (5% default), eliminating contrast
               jitter.
           o Added new gamma mapping option for better image rendering control.
           o Added 99:1 contrast mode to auto map - ignore outliers to create more vivid
               images.
      Utility and Device Support
           o Added Imaris launcher button to effortlessly transfer the current iQ image into
               Imaris.
           o Updated AxioObserver Support
           o Defaulting image disk full warning to 75%.
      Python
           o Added load, save and manipulation of colour LUTs in Python
           o iQImage class now allows frames from a multidimensional iQ image to be
               iterated with nframes(), frame(n) and nframe2position(n) functions
           o Updated Python documentation.


Bug Fixes

      Fixes min and max scaling and graph disappearing in Line Profile tool
      Fixes camera "More tabs" behaviour
      Fixes crash on Ctrl+F4
      Fixes system freezes when using Clara and running long protocols.
      Fixes checkerboards appearing during channel changing / Z protocols.
      Fixes separate taskbar item for some plug-ins.
      Fixes camera rotation causing protocol not to work.
      Fixes several GUI layout/format errors.
      Fixes for ASI Stage registration problem.
      Fixes failed allocation not exiting cleanly
      Fixes poly-line FRAPs for Andor FRAPPA
      Fixes possible division by zero error when exposure time is very short
      Fixes memory issues with background correction - more efficient structure.
      Fixes default pre-amp gain (now highest)
      Fixes default exposure for Andor camera (now 30ms).
      Fixes memory leaks.
Andor iQ Release Notes

      Fixes AOTF control intensity - now updates if changed from any part of iQ.
      Fixes FRAPPA channel behaviour when switching between configurations.
      Fixes crash when re-running montage scan after montage offline processing.
      Fixes some protocol tree rules, inserts and deletes.
      Fixes crash when starting protocol with autofocus.
      Fixes Protocol Elapsed Time sometimes starts at a large value.
      Fixes Online Chart loses data once Events window is closed
      Fixes 4th LED control for CoolLED
      Fixes ALC Sapphire laser initialisation error.
      Fixes Dual FRAPPA device selection has one device not visible
      Fixes access violation on live/idle/snap.
      Fixes MicroPoint bleaching at end of protocol - ensures it will stop when protocol
      finishes.
      Fixes for copying protocols and iXon shutter not opening.
      Fixes connection to bad COM ports for Lumen Pro and Andor PZ.
      Fixes Andor camera initialisation - fixes live not working first time on new
      configuration.
      Fixes trigger in and out.
      Fixes initial position on FRAPPA calibration wizard.
      Fixes FRAPPA Calibration auto-point move.
      Fixes Enter key not working when using Region Histogram.
      Fixes Python shortcuts.
      Fixes Python shell not allowing characters to be deleted.
      Fixes Python progress bars issues.
      Fixes Python image pixel array assignment.
      Removed some distracting Python warnings.
      Fixes Python imagedisk.clear() call.
      Python IDE now runs as a separate process to iQ
Andor iQ Release Notes


Andor iQ 2.1
September 2010

Introduction

An incremental release following iQ 2.0 including key bug fixes and desired features.

New Features

        Reference Z – Allows the focus Z position of particular XY positions to be stored as
        part of the scan. The Z scan then operates relative to this position ensuring focused Z
        stacks at each XY scan location.
        FRAPPA SDK 2010 – with this new SDK release our FRAPPA system can upload the
        ROI data 7 times faster before it begins frapping. Please contact
        confocalsupport@andor.com for a free firmware upgrade to take advantage of this
        exciting development if you have an older FRAPPA system.
        Image automap is now defaulted to sampling “All” pixels to produce smoother, less
        flickering displays


Bug Fixes

This interim release addresses some critical issues reported by our customers and internal
QA team.

        “Access Violation” error when lone Snap inserted in protocol tree
        Editing binning in protocol tree produced "Not a Valid Floating point Value"
        Repeated Move, Snaps in the protocol tree results in only one frame per channel
        Updated support contact information in About box
        Manual FRAPPA not working during experiment
        Live progress view only shows the last Z frame during an XY scan with Z repeat
        "Default Calibration" warning message now only appears once a minute
        Fixes floating point error message which stopped images being opened.
        Allow control of Andor PZ in XY scan wizard
        When defining XY fields using Andor PZ for Z, adjustment values were too coarse
        Fixed calibrate of Andor FRAPPA when using 1.10.3 executable
        Fixed intermittent timeouts in camera
        Fixes KI_MM40 access violation
        Mosaic failed to calibrate following installation
        Camera temperature was not updating after a protocol was executed
        Speeded up camera acquisition
        Fixed bug in dual camera when loading protocols with “Load Protocol”
        Fixed potential crash when Ratio wizard acquires preview frames
        Fixed bug where Ratio wizard does not correctly generate Ratio histogram
        Sigma Koki stage can now be selected as the current XY device
Andor iQ Release Notes


Andor iQ2
       st
July 31 2010


Introduction to iQ2

We are delighted to announce the release of iQ2, which opens new vistas for iQ users. iQ2
delivers new flexible acquisition Protocols, a Python Integrated Development Environment
(IDE) and improvements in GUI look and feel. iQ2 also integrates support for Photonic
Instruments Mosaic and MicroPoint photo-stimulation devices extending our systems to
enable simultaneous imaging with FRAP, PA and ablation actions. Flexible Protocols allow
multi-phase bleach and activation experiments, greatly simplifying setup and operation of
FRAPPA devices.

New flexibility in iQ2 Protocols allows us to unify the iQ2 acquisition user interface. This
simplifies training and application of iQ2 for new and occasional users, removing confusion
between time-lapse and FLZ modes. It also means that we can focus our development
resources on optimizing performance of time lapse Protocols and the user interface to the
Protocol Tree.

iQ2 maintains backward compatibility with iQ 1.10.3 with the following possibilities: switch
between versions as desired; operate with existing Configurations; import existing Channels,
Protocols and Scans.

Co-operation with Imaris 7.1 has been improved with Imaris now able to read the iQ
ImageDisk directly. This capability removes the delays caused by the save and open
sequence usually associated with file transfers from third party software and lets you focus on
more important analysis tasks.

We encourage users to contact us with their feedback on this new release. We are committed
to the ongoing development and improvement of iQ software.



New Features in iQ2

Flexible Protocols – iQ2 now enables you to build a virtually endless range of acquisition
sequences. Because iQ2 supports nesting and sequencing of Repeat loops, it is possible to
acquire data in “sparse” or “irregular” patterns. So for example, you can create a multi-phase
acquisition for “baseline-activate-response” with different acquisition rates in the different
segments of the Protocol and you can acquire one Channel in the baseline phase and the
same or other Channel(s) in the response phase.

Constructor - Use of sparse and irregular acquisition patterns has an impact on the “shape”
of resultant data. To manage this images are now created Channel by Channel. This means
you will see more images on the ImageDisk for irregular Protocols and you can access
these independently. However iQ2 also creates a Channel combination data structure, which
organizes the Channels in relation to each other for direct view or analysis of the entire data
set. We call the combination structure “Constructor” and it consists of a collection of pointers
to the data so that they can be accessed fast and in a sensible sequence, while at the same
time not duplicating storage requirements. When you look at the ImageDisk after an irregular
acquisition, you will see the Constructor at the top of the list with the individual Channel
images listed below the constructor and with a number in parenthesis (n) which specifies its
acquisition order.

Sequential and Nested Repeats - Repeat keywords (loop or iteration) have been extended
to include not only Time (with Interval), but also Channel, XY (with Montage and Multi-Well)
and Repeat Z. While the Repeat XY, and hence Montage and Multi-Well, remains a singleton,
multiple Repeat Z actions can now be used in a single Protocol and each uses relative
Andor iQ Release Notes

coordinates. Time, Channel and Z Repeats can now be sequenced and nested to allow
complex multi-dimensional acquisition e.g. multi-phase acquisitions; nested slow and fast time
acquisitions; Time nested within XY Repeats to allow time lapse or burst acquisition at
multiple fields of view. The possibilities are extensive.

Mosaic and MicroPoint - since Andor acquired Photonic Instruments at the end of April
2010, we have worked with PI colleagues to bring these exciting products into the iQ
framework. This has now been completed to a first release status. We have extended the
FRAPPA Calibration Wizard to allow alignment of both Mosaic and MicroPoint, while the
existing activation and ROI interface also supports the new devices. We have implemented
an asynchronous FRAPPA action to allow simultaneous execution of imaging and FRAPPA
actions and to support the “zero delta T” model of Mosaic (http://www.photonic-
instruments.com/Digital_Illumination.aspx) and MicroPoint (http://www.photonic-
instruments.com/MicroPoint_Computer_Controlled.aspx) actions.

GUI improvements - the iQ2 GUI has been refreshed and brought a little more up to date.
We have introduced new icons and provided Hints and Help for keywords in the Protocol Tree
and Insert options. In the iQ2 Control Window we have removed the static information held in
the “Current Context” region and placed the user and Configuration in the Help\Configuration
menu item, while the image details (name, type, size, calibration) are now stored in the Image
Window title bar. This frees up space at the top of the Control Window for a Toolbar
containing Open, Save, Live, Snap and Channel buttons. This is an ongoing work and other
changes will be forthcoming.

Backward compatibility - iQ2 is backward compatible with version 1.10.3 and as stated in
the introduction allows you to operate with existing Configurations and import Channels,
Protocols and Scans from those Configurations. For speed, FLZ still has the edge (and you
can continue to use 1.10.3 if you desire), but in the future releases the speed difference will
be quickly eroded as we continue to streamline and multi-thread Protocol execution.

Python IDE - the integration of Python with iQ has been a long term goal and finally is
realized in iQ2. Python is an open source scripting or programming language with a strong
following among scientific and technical computing users - see www.python.org and
www.scipy.org. Python offers a powerful resource to those who want to implement their own
algorithms or extend iQ2 capabilities. To help achieve this we have created a Python coding
environment as a Plug-in to iQ2 making launch and connection to Python a simple act. We
have also created an iQ2 database object (iQDB) which allows Python access to the
ImageDisk and an iQ2 image object which supports exchange of data between iQ2 internal
format and Numpy arrays - multi-dimensional data matrices supported under Python
Numerical processing libraries.

Note that the Python IDE is an optional feature and requires download of Py-iQ, comprising
about 220 MB of open source and proprietary object modules. Py-iQ will be on CD for new
licenses and downloadable for installation on your system or computer.


Future iQ Strategy

Py-iQ web resources - Now that Py-iQ is released we intend to build web-based resources
(e.g. User Group) to allow scientists to share and exchange Python code and applications
knowledge relating to image acquisition, instrument control and image processing and
analysis. We will advise users when this becomes available and would welcome suggestions
on where and how to best host this resource.

iQ and Imaris - one of our goals in the wider development strategy is to allow iQ and Imaris
to cooperate smoothly and focus on core functionalities. In this way we can avoid duplication
of effort and use our development resources to maximum effect. In future releases we expect
to remove some functionality from iQ which is better addressed in Imaris. For example, basic
on-line 3D/4D visualization will be retained in iQ, but for serious off-line work Imaris will be
preferred because it has much more advanced capabilities such as surface rendering. We will
Andor iQ Release Notes

continue to develop the products in this context and welcome user feedback on new features
requests.

Thanks for your continued support and feedback.
The iQ Team
Andor iQ Release Notes


Andor iQ 1.10.3
       st
June 1 2010


Introduction

iQ 1.10.3 – provides a number of important improvement and fixes.

Features and Fixes in this release

FRAPPA major speed up – FRAPPA has received a major improvement for interactive use
by speeding up the communication with the device controller. Upload times have been
reduced by a factor of approximately seven (7X). The result is a significant enhancement in
performance and usability. When coupled with the FRAPPA All and Single parameter
described below FRAPPA users will sense an major benefit.

To receive this free of charge upgrade, you should contact Andor or your local
representative to arrange a remote support session. One of our skilled service personnel will
update your FRAPPA system firmware as well as providing a new FRAPPA library. Once
updated, you will have immediate access to greatly improved performance.

FRAPPA - new parameter - the FRAPPA keyword has a new parameter which can take
values Single and All. These two specify when a FRAPPA actions is initiated that either the
currently selected region (Single) or All regions (All) in the image window are FRAPPed.

Nikon TiE SDK update– changes to the Nikon TiE SDK drivers changed the way the Z
device values are communicated to the application. This has now been changed in iQ and is
fully functional after testing with SDK version 4.2.3.572.

Nikon Intensilight – We have now included control of the Intensilight metal halide light
source. The shutter will need you to introduce a Transition Delay of ≈ 50-100 ms for reliable
shutter synchronisation. It is however, better to use an external fast shutter for this operation.
Run the Intensilight as a stand alone USB device, not from the TiE hub.

Low Cost Breakout Box (BoB), DIO24 – We have made changes to FLZ to allow operation
without a DAC PCI card if no analog control is required. Instead a DIO24 PCI card can be
used and TTL input and output can be used for trigger input sensing and outputs. A new Low
Cost Break out Box has been designed to be compatible with this configuration, which will
function with Trigger and Event device as well in the FLZ mode.

Mad City Labs 3-axis piezo stage support - has now been implemented in iQ via USB 2.0
connections. For more details please contact Andor or Mad City Labs. The tested stage had a
motion range of 200 um in X,Y and Z. Mad City driver version 1.7 (March 19 2010) is required
for this functionality and is normally supplied with the stages.

Time Interval Error – A bug has been found and fixed in the Time-lapse Loop timing. The
error could result in ≈200 ms errors.

FLZ and Monochromator – Changes in FLZ for version 1.10.2 had broken the connection to
Monochromator devices. This has now been restored to operation.

Stage Hunting – closed loop stages offer high accuracy because the have a position encoder
included in the sensing loop. The systems try to achieve zero error between the demand
position and achieved position. Mechanical limitations mean that this is a goal rather than a
guaranteed result. We added a feature in version 1.10.2 to generate a warning Event if the
residual error exceeds ± 1 resolution unit. This turned out to be too stringent and as a result
iQ generates Events for many installed stages. We have now reduced the target to ± 3
resolution units and made the setting accessible to the user for adjustment if desired. To
Andor iQ Release Notes

access the setting select the menu item Wizards/Select XYZ device and adjust the Stage
Tolerance value (in stage resolution units).

Andor camera SDK update - A new SDK is included in this release which supports the Clara
and new Clara E cameras.

“Cannot communicate with card error” - Andor camera controller card CCI-23 has a
firmware upgrade (version 291) that fixes this annoying problem, which can occur deep into a
time-lapse Protocol. This upgrade resolves the problem finally. Apologies to all those who
have suffered!

Known issues at time of release

Sutter L10-B controller firmware BUG – In the Sutter L10-B controller there is a reset bug
which will cause an error in filter positioning after a reset – this happens whenever a step is
missed in positioning. The bug may show up in time lapse imaging, when you may see loss
of filter position synchronisation at some random time point in the Protocol execution.

Sutter fixed this bug in firmware version 2.22. Please check that your controller firmware is at
least on version 2.22. We investigated reading the firmware version from iQ to provide an
active warning, but it is not available in the Sutter communication protocol. So you have to
check it on the controller display at start up. If the firmware is earlier than version 2.22 please
contact Andor or your local representative and we will arrange for exchange of the controller
direct from Sutter. Unfortunately the firmware cannot be updated remotely.

Olympus BX61 – IQ connection to the BX61 disables the motorized focus and condenser
top lens. This will be addressed in a future version of the software.

FLZ with Frame Transfer (FT) – Because of the timing sensitivity of frame transfer, users
should note that there are some restrictions on its use.

   FLZ with FT should only be used with a Burst >1 if the Burst interval is set to zero
   (minimum). If you set a Burst interval > the minimum Burst Time, then a bright frame will
   result at the start of the next Burst.

   FLZ and Frame Averaging – FLZ is intended for high speed (and Burst) acquisition. We
   have therefore disabled frame averaging in this mode. If you wish to carry our frame
   averaging then switch to Time Lapse operation.


Thanks for continued support…
Andor iQ Release Notes


Andor iQ 1.10.2
          th
March 12 2010


Introduction

iQ 1.10.2 – More fixes and features – this iQ 1.10.2 update provides a number of
improvements and fixes for the 1.10 platform.

Features and Fixes in this release

The “Current” Channel –
“Current” channel first presented with iQ 1.10 was greeted with mixed reviews - some love it
and some hate it. Hence we have now made it an option with a new Options dialog accessible
from an Options button on the Acquisition tab. The user can select whether channel reverts to
Current or last used channel at the end of a Protocol. We hope this will satisfy everyone.

Huge Allocations
A bug was found with allocations exceeding 250,000 frames, which must have been present
for some time, but had not been exercised. Now the maximum number of frames that iQ can
allocate in a single acquisition has been extended to 997,952. That’s 2048 below 1 million
frames, the maximum we have previously quoted. Those files are used for house keeping on
the ImageDisk.

Wait for Allocation
The new threaded image allocation feature Wait for Allocation On/Off could fail if the
allocation was aborted. The termination failure left the allocation thread running which could
cause problems later. This has now been resolved.

Dual and Multi Camera Use
The use of multiple cameras in iQ has been cleaned up and improved considerably. When
using different cameras in different configurations a bug was reported in which the
identification of the cameras could become confused. In addition when using multiple
cameras in a single instance of iQ and switching between cameras identification errors could
also arise in some cases. This version cleans this up and should remove any problems
relating to multiple camera management. We have tested in 2 and 3 camera setups using
mixed and identical cameras.

Autofocus Improvements with Scans
We have extended the use of Autofocus (PFS, ZDC) with Scans and ensured support of a
wider range of user requested use cases. The following cases are fully supported.
                1. Initialize Autofocus at every field to a new position;
                2. Initialize Autofocus at the first field and use refocus at all subsequent fields.
                3. Initialise Autofocus once at first field and then leave it unchanged for
                subsequent fields.
IQ now supports Autofocus correctly in all these cases and functions correctly whether the
microscope Z stage or Piezo is the selected Z device.



Autofocus Events
In some cases we have observed Autofocus failures during long term experiments.
Customers have also reported this. We believe this is due to optical changes in the specimen,
drying out of medium or immersion fluid among other things. Previously if this occurred iQ
would continue to attempt success and could delay or even stop progress of the acquisition
sequence. In the current release such a failure is handled as follows. iQ allows the protocol to
continue, but only after we acquire a frame at the last successful Z position and an Event is
Andor iQ Release Notes

logged in the image at the current frame. In this way iQ notes the failure, but does not stop
acquisition of subsequent data.

XY stage Closed Loop Positioning Timeout
In closed-loop stages some users have observed positioning time-outs when the stage servo
window is set too tightly. In these cases the stage can “hunt” (or try to reduce the positioning
error) for long periods and in the worst case never achieve the error criterion. Previously iQ
would throw a time-out and show a message box, which blocks progress of the Protocol. Now
we adopt a similar scheme to that with Autofocus – we record a frame (or stack) at the current
XY position and then log an Event in the image metadata. In this way the user will be aware a
time-out has occurred, but the Protocol will not be blocked and will run to completion.
Numerous Events will indicate an incorrect servo window setting and in extreme cases a
stage problem.

Dual ImageDisk
The use of two camera simultaneous capture via two instances of iQ uses the Dual Image
Disk plugin to merge the resulting datasets into 2-channel data of the appropriate
dimensionality. A bug was reported in which two single frames could not be merged. This has
been fixed and the investigation led to other improvements such as now allowing the
dimensionality of the data to be defined by either local or remote image depending on which
shows the higher number of dimensions. Look up tables and mapping data are now inherited
in the correct way.


FLZ enhancements and fixes
  FRAPPA with FLZ – We have reviewed and rewritten the user guide explanation of how
  to setup FRAPPA with FLZ as this was rather confusing. In addition we have provided an
  Option to avoid the popup of the FRAPPA Event dialog at the end of a Protocol. This
  removes the possibility of blocking a Load Protocol action and is accessed via the Options
  dialog on the Acquisition tab.
  FRAPPA with FLZ – One user reported that FRAPPA All Regions options in the Image
  Window right mouse menu did not function. This has been tested in the current version
  and found to be functional.
  Laser intensity information was not included in the image header if the “After Burst”
  setting was not used. This has now been fixed so that laser intensity data is recorded in all
  cases.
  Fast Scan removed – A bug has been reported in Fast Scan mode regarding switching
  exposure times. In Version 1.10.1 we improved the FLZ mode to monitor exposure in
  software, so there is no longer any need to utilize Fast Scan mode and so we have
  removed it from the options.
  MPU Port interference – we have fixed a random port switching bug sometimes seen
  when switching into Live mode.
Andor iQ Release Notes


Andor iQ 1.10.1
          rd
January 3 2010


Introduction

iQ 1.10.1 – Happy New Year – following the release of iQ 1.10.0 we bring this update to
provide a number of improvements and fixes we have produced after release. These have
been prompted by our own testing and use, but also by user feedback. This release continues
the rise in performance and flexibility of iQ’s FLZ mode as well as wider capabilities of the
platform as a whole.

New Features in this release

FLZ enhancements and fixes
  Integration with FRAPPA has been simplified by way of the After Burst settings (now on a
  new dialog) allow the user to set not only the Z and laser wavelength, but also the laser
  power and MPU Port. Thus when FLZ returned control to iQ, it can set the system
  hardware to the defined Z position, select the laser line and power and set the MPU switch
  to FRAPPA in preparation for a FRAPPA action on selected regions. When iQ returns
  control to FLZ it automatically returns the MPU to the previous setting and continues
  imaging.
  Burst control now has an Interval, so that fast LZ scanning can be used for time lapse at
  single or multi-field positions. This is required for specimens which are sensitive to motion,
  but where researchers would still like to obtain time-lapse LZ stacks at multiple fields over
  time.
  Autofocus control (AFC = Nikon PFS or Olympus ZDC) can be used correctly with FLZ
  and Z scanning. Please note you must initialize AFC at the same Piezo stage plane as
  that set in After Burst, otherwise AFC results will be offset from the desired plane.
  Bright field settings have been extended to include exposure time and emission wheel
  position if required. The Interval can now be defined at any frequency. The Bright field
  image can be copied to all Z planes in an image or simply at the plane collected. It will be
  copied to all time positions to provide a reference in subsequent visualizations.
  Emission filter wheel support has been extended to any wheel on the Sutter 10-3 control.
  This allows the wheel on port 3 to be used while ports 1 and 2 can be used for shutters.
  Laser power settings are now saved in the Image header along with other FLZ
  information.
  To reduce Mapping issues using the Current channel, the user normally selects Automap.
  To reduce overheads and help with performance we now display only images from the first
  channel during an FLZ burst.
  Frame Transfer has been reintroduced with FLZ. With fast machines (e.g. Core i7
  processors) the FT mode functions well, but because of the potential for time variations in
  the operating system, you may still see some variations in exposure resulting from
  software based timings.

XY and Z Scanning
  The Move To function of the right mouse menu in the image Window, was sometimes
  broken in 1.10.0 and has now been fixed to work with all the new scan modes.
  We have added Set Reference to the Move To menu option. Move To by default moves
  the identified feature to the centre of the field of view. Set Reference allows another point in
  the field to be specified as reference and supports setups where a fixed beam device (e.g.
  an ablation laser) is used at the Reference point.
  Scan editor now has the option to reposition in Z if the user selects the option. The
  default setting is off to avoid unwanted focus changes or objective specimen damage!
  Autofocus control (AFC = Nikon PFS or Olympus ZDC) can be used correctly with FLZ
  and Z scanning. Please note you must initialize AFC at the same Piezo stage plane as that
  set in After Burst, otherwise AFC results will be offset from the desired plane.
Andor iQ Release Notes

  The Stage Registration dialog which appears at start up could be cancelled, but would
  rather frequently be shown again. We have added the ability to suppress the Registration.
  When the user wants to perform a Montage or Multi-well scans, the Stage Alignment and
  Registration must be completed since we require absolute stage coordinates.

Fast MIP and 4D View Plugins
  We have extended both these plug ins to allow simultaneous use. They both have the
  option to “Stay on Top” and now have an update button on the GUI to allow them to be
  resynchronized with the main Image Window when working with multi-field or multi-well
  data sets.

Selector and Dimension Editor Plugins
   Fixes have been made to these plugins to ensure correct operation with new scan formats.
   Selector now ensures that wavelength dimensions have correct mapping and LUT settings
   in the multi-dimensional sub-regions. This also corrects a bug seen in Multi-load of data
   from external progams, which could result in black (zero) frames.
   Dimension editor has been enhanced to allow editing of Wavelength dimension name and
   stamp values. This allows correction of images with identical channel stamp values
   (possible prior to iQ 1.10) for subsequent processing and analysis.

CSUX 12 position filter wheel
  Yokogawa’s new 12-position filter wheel is supported in this release. The wheel is
  manufactured from magnesium alloy ensuring a low mass. This allows switching times
  between adjacent positions to be as low as 33 ms. The filter wheel is externally mounted
  from the CSUX and can be bolted down to the optical table to minimize vibrations.


Bitplane AG acquired by Andor December 23rd 2009

It is with great pleasure that we announce this acquisition. Over the coming years we will
harness our combined resources and efforts to bring these software platforms together and to
offer the best solutions in image acquisition and analysis to back up our world-class hardware
and systems technologies.

Happy New Year from all at Andor!
Andor iQ Release Notes


Andor iQ 1.10.0
            th
October 30 2009


Introduction

iQ 1.10.0 marks a major step towards the release of iQ 2 and brings together some key
features and enhancements which brings many new benefits and requested features to the
software. In this release we prepare for iQ 2 functionality by enhancing many facets of iQ’s
operation and flexibility, enabling dual camera simultaneous acquisition in a single PC,
extending the application of FastLZ module, dramatically improving Scan flexibility and
changing the way that Protocols are constructed and executed.

All this helps to pave the way for more flexible Protocols in iQ2 and provides a means of
monitoring Protocol execution progress in the Python programming environment. Exchange of
data between Python’s Numpy arrays, iQ ImageDisk and the HDF5 open file format will allow
users to code iQ-Python extensions for image processing and real time control. But for those
Python capabilities we must wait for iQ2, which is now scheduled for release in March 2010.


New Features in this release

Protocol Tree changes –
We have removed the Protocol Wizard from iQ 1.10.0 since it was a source of some
unnecessary limitations and could lead to erroneous labelling of Channels in a Protocol. Now
the User Creates a basic single channel Protocol with the Protocol Manager New button.
Time lapse protocols allow channels and scans can be inserted at the desired locations in
the Protocol Tree, while FLZ protocols now accept XY Scans by insertion, with channel and
Z scan control managed from the FLZ Sequence tab. If the user wants to make a multi-
channel Protocol, then at least two channels must exist or be created as usual with the
Channel Wizard and then inserted into the Tree.
All operations on the Tree are now handled from the right mouse pop-up menu, enabling
Insert and Delete. Scans can be inserted in the same way. In future, this same mechanism
will be used to Create Protocols of much higher complexity and flexibility to address user
needs.

We also added the new Protocol key word Wait for Allocation ON/OFF – which allows the
user to specify whether to wait for iQ to finish allocating on the ImageDisk before starting the
protocol (ON) or to start while allocation proceeds (OFF). This required the threading of the
ImageDisk control and is helpful to avoid a long delay before starting with large data sets e.g.
overnight runs. Although this has an impact on performance until allocation is complete, the
convenience outweighs this when speed is not of the utmost importance. Also note that Load
Protocol now can be issued and the Protocol execution started much more quickly with this
setting off.

The “Current” Channel – guards against inadvertent channel edits
IQ now defaults to using the “Current” channel in the base Protocol, which uses whatever
current settings are shown in the Device Setup dialog. This means the user can acquire
data without first defining a Channel, simply by setting up the required values in the Device
Setup tabs. The other benefits of the “Current” Channel include isolation of user-defined
channels from inadvertent changes. At the end of Protocol execution iQ switches the Device
Setup to “Current” and any changes in the GUI cannot be applied to another channel without
its explicit selection.


FLZ fixes and enhancements
The FLZ module has been improved to allow operation with various hardware devices, where
it was previously restricted.
Andor iQ Release Notes

                 New Protocol control of FLZ – when a Protocol is defined as FLZ, iQ
                 creates an FLZ settings file of the same name and stores the current FLZ
                 parameters into it. When the Protocol is executed iQ initializes FLZ to those
                 settings. This can be updated by the Save option in FLZ so the user can
                 invoke execution of given set of wavelength, exposure and Z scan ranges
                 without the need to reprogram the FLZ Sequence GUI.
                 FLZ can now be used to capture LZ bursts at multiple-XY fields, whether in
                 multi-well plates or multi-point sequences. This feature has been frequently
                 requested and now finds its way into the feature list.
                 Burst capability extends the Timing control tab to support more flexible
                 programming of synchronized changes in TTL output signals e.g. for
                 perfusion control or laser shutters. Burst acts as an inner control loop and the
                 Protocol Repeat as the outer, allowing us to generate repeating control
                 sequences in which 3 Burst TTL signal can be triggered on and off at
                 arbitrary points in the Burst. The outer Protocol Repeat defines how many
                 times the sequence will occur. This can be considered as a “Ring”
                 operation used for sequential laser wavelength exposures each with a user-
                 defined period and the sum of exposures being equal to the Burst value.
                 Acquisition of bright field (e.g. DIC) images at user defined Z position has
                 been extended to function with 200, 250 and 500 um Piezo device ranges as
                 well as 100 um.
                 We have improved the synchronization issues with using Frame Transfer
                 (FT) in FLZ. FT was removed to avoid the risk of bright or over-exposed
                 frames in the FLZ sequence, resulting from Windows software latencies
                 which can delay External Trigger signals being sent to the camera. This
                 feature has been made more robust and is available to meet user speed
                 requirements. Better FLZ execution sequencing and faster multi-core
                 processors have contributed to reduce the risk of such errors.
                 FRAPPA can now be operated with FLZ and also specify a Z plane for
                 FRAPPA action known as the “Resting Z position”. This change makes it
                 possible to implement fast LZ scanning alongside targeted 3D FRAPPA on
                 user-selected regions.

Simultaneous high performance two camera acquisition can now be done on a single
PC using two instances of iQ 1.10.0. One instance is run as FLZ Master, while the second is
run as Fast Slave. Both cameras must be set to External Trigger mode in their respective
instances of iQ 1.10.0. The Master is setup to Run a single wavelength FLZ protocol (N
repeats, Z z-steps), while the second is setup to Run a single channel Fast protocol with M
frames, (with M = N x C x Z). The Master camera is triggered from PCU output D07, as
normal and the Slave is triggered form the Master Fire pulse. The images can be merged into
2 channel, ZT series using the Dual ImageDisk Plugin as documented in the new iQ 1.10.0
user guide. In this way our tests on a dual core mid range Dell PC we have achieved
performance which approaches (98%) of single camera execution running at full speed. For
best performance we recommend use of a dedicated dual disk RAID 0 configuration for the iQ
ImageDisk.

Major Improvements to Scan Capabilities and User Control of Scanning
       Rationalization of Scan setups now allows the creation of multi-well patterns, called
       Plates. When a Plate is used for a new scan sequence, the user defines the Origin
       of the first well (top left coordinates). If the orientation of the well plate is not parallel
       to the stage axes for any reason, then the “Skew” can be compensated by specifying
       a second coordinate pair of another well on the same row as the first e.g. second or
       last in that same row. The skew will be used in computing the correct XY coordinate
       sequences to ensure accurate scanning of the Wells.
       The multi-well scan can be further modified in the definition phase, with a user-
       specified list of Wells to be Included or Rejection from the scan. This can be
       because the Wells were not used or because the specimen did not behave as
       required e.g. the cell colony died or did not transfect. The Rejection list is specified
       in a simple user interface step and specified by sequences like this - “9, 10, 11, 15-
       18, 21-24”.
Andor iQ Release Notes

         The multi-well scan can now be setup to include an Autofocus offset (ZDC or PFS
         value) for every well or field in each well.
         Systematic sampling can be applied at all wells as previously possible.
         In Multi-field or Multi-point imaging the user can also add an Autofocus value on a per
         field basis.
         Montage is also extended to include Autofocus settings on a per field basis. ??
         In all Multi-well and Multi-field cases Montage can be specified at each field
         position, with the position taken as the montage centre.
         To implement Montage scanning at each field we have introduced the Montage
         dimension into the image to allow ease of Navigation?
         When a scan is being defined, edited or executed in a Protocol iQ now creates a
         graphical view of the scan pattern (including wells and montages if present) and
         shows the user where the stage/camera is currently, in relation to the pattern defined.
         This is a most helpful addition to interpreting/monitoring progress.
         The Z Registration step of Stage Registration, at iQ startup has been removed. Now
         the user just needs to “Focus the First Field” of a scan before running a Protocol
         which includes an XY or XYZ scan.

Clara – Andor’s latest high performance CCD camera,
Clara utilizes the Sony ICX285 sensor and offers 1362x1040 pixels with 6.45 um square
pixels, matching the Nyquist sampling criterion with high resolution 60X and 100X objectives.
The camera benefits from our new Volvac technology, vacuum sealing the chip for unrivalled
fan-assisted cooling to -45C, and long term sensor environmental stability. Without fan
cooling, a must for electrophysiology and other vibration sensitive applications, the
camera can maintain a stable sensor temperature of -20C.
Clara is interfaced to Windows PCs with the industry standard USB 2.0 (480 Mbps) and
uniquely offers three read out speeds to allow trade off between frame rate and read noise,
with figures respectively of 1 MHz @ 3 electrons rms (e), 16 bit resolution; 10 MHz @ 4.5 e,
14 bits; and 20 MHz @ 5.5 e, 14 bits. The exceptionally low read noise of 3 e at 1 MHz
delivers industry-leading dynamic range of 7000:1 and makes full use of the ADC bit depth.
Clara provides flexibility, compact design, unrivalled cooling and is the top performing CCD
camera in the microscopy market. iQ 1.10.0 provides full control of all Clara features,
including “deep depletion mode” which extends its red performance beyond 800nm. iQ 1.10.0
supports Clara in both Time lapse and FLZ modes.


ImageDisk – in order to achieve the simultaneous acquisition from two cameras, we have improved
management of memory and the shared ImageDisk. Image writing functions have been threaded to
allow each instance of the software to operate without blocking the other. We have also threaded the
image and time stamp allocation processes to virtually remove the start delay when running a
Protocol with a large number of frames. This also substantially removes transition delays when
using Load Protocol to build more complex Protocol sequences.

ImageList - we have changed the presentation of metadata in the image details section to reflect the
protocol tree rather than an internal array structure. This makes the information much more readable
and easily interpreted. In addition, the presentation of image name and path has been cleaned up to
improve the user interface and ease the finding of images in the list.

Andor SIF file– Andor’s SIF files are generated by Solis when streaming mode kinetic series to disk.
Since Solis can run all Andor cameras at the full potential frame rate, including “virtual chip” mode at
thousands of frames per second, it is the most efficient way to acquire when raw speed is the primary
goal. From version iQ 1.10.0 onwards we can guarantee compatibility with Solis SIF files via shared
libraries, thus ensuring smooth translation between the two programs.

Field Split Plugin – now allows for Rotation with split field images as well as dual camera images.
Andor iQ Release Notes


Filter Plugin provides a set of 3x3 convolution based filters and has been fixed to correctly handle RGB
image types such as AVI and BMP. This plug-in also provides 3 neighbourhood ranking filters, Median,
Erode (min) and Dilate (max).

Format Converter (Image Edit menu) now supports RGB split, which creates a 3 channel 8 bit image
from the 24 bit type, assigning Red, Green and Blue pseudo color look up tables to the appropriate
channel.

Montage PlugIn has been enhanced to support the Multi-field or Multi-well Montage case outlined in
Scan improvements above.

FRAPPA – performance has been improved by threading the computation and execution to reduce
blocking the rest of iQ.

Olympus ZDC – we have improved the ZDC user interface and reporting to provide better feedback
and advice to users. During operation the ZDC dialog shows “amber” and when it completes
successfully the dialog shows “green”. On the other hand if the process fails then the dialog shows
“red”, indicating it was unable to “find” the air-glass or glass-medium interface. ZDC supports a subset
of the Olympus objective range, so if ZDC fails because the objective is not supported, then iQ shows a
suitable text message to this effect. The result is a more informative and friendlier operation.

Ludl MACX000 controller - we have worked with Ludl over the last few months to implement control of
their new MAC6000 controller into our Ludl control adapter. In addition, we have added user interface
components to allow selection of Closed or Open Loop operation and setting of Stage Axis Speed and
Acceleration profiles. In this process, a long standing communications timeout bug was discovered,
which has now been fixed and results in faster filter wheel movements.

Bug Fixes
        Reading of a series of single TIFF files could result in frame time or Z stamps having the
        same value throughout the series. This has now been fixed.
        Dimension Editor in the Image Window Edit menu has been enhanced to allow editing of
        Channel names and values. In previous versions of iQ this bug could arise and then images
        would not be accessible to processing because of duplicate channel stamps. This can now be
        rectified, and is no longer possible in iQ 1.10.0 since the Protocol Wizard has been removed.
        Selector could mangle LUTs and channels names or values. This bug has been fixed.
        Dual ImageDisk PlugIn has been repaired to avoid mangling channel names, LUTs and
        values.
        The interactive Mapping dialog could result in an exception on the exit from iQ if left open.
        This bug has been resolved.
        The Max Timeout setting is intended to define the duration of countdown dialogs which give
        the user an opportunity to switch software action e.g. “Redefine Scan Range”. The setting
        failed to function correctly, but has now been resolved.
        Maximum Exposure of Andor cameras has been set to 120 minutes, whereas it was
        previously 60 minutes.
        Channel DeltaZ allows each channel to be offset relative to others in a Protocol, correcting for
        chromatic aberration or adjusting to the plane of features of interest. This feature was bugged
        and now is fully functional and performs with Z scans also.
        FRAPPA Channel DeltaZ has been added to allow for FRAP and PA actions at a preferred Z
        plane in Time Lapse mode.
        FRAPPA Events and ROI coordinates were jumbled in the Image Header. This has been
        fixed.
        Unable to Communicate with Card error has been fixed and was due to a timeout value not
        being updated when exposure time exceeded 600 ms.
Andor iQ Release Notes


   Last, but not least our friends at Bitplane have implemented improved the speed and interpretation
   of the Andor Multidimensional TIFF files in Imaris 6.4, which releases at the end of October. As
   an example a large 5D data set which previously took 13 minutes to load has been bench marked
   at 2.5 minutes by a user at MPI in Dresden.


   We sincerely hope that the substantial improvements reported here will make the lives of our users
   more satisfying and productive. Please keep advising us of things you would like to see and
   frustrations or problems you face so that we can continue to improve the product.


   Warm Greetings from

   The iQ Development Team in Belfast and North Carolina.
Andor iQ Release Notes


         Andor iQ 1.9.1
         rd
April 23 2009


Introduction

iQ 1.9.1 is an intermediate release, provided as an interim before iQ 2 is released later this year. The
main issues addressed are new device controllers, bug fixes and some improvements to scanning multi-
well or micro plates.


New features in iQ 1.9.1

Andor ALC-UVP-350 is a new controller for a 350 nm, 60 uJ, 5ns pulsed UV laser device. This unit can
be used for ablation or cutting and when power is reduced for uncaging and spot photolysis. For more
information on the UVP instrument follow this link.
http://www.andor.com/microscopy_systems/peripherals/laser_combiners/?docID=896

The Stage Alignment Wizard, required for Multi-well and Montage scan operations, developed a bug in
the last release and has now been fixed. This enables alignment of the camera X and Y axes to be
parallel to the motorised stage motion.

Multi-well or Micro Plate Scanning - we have fixed a scan orientation problem when working with
back illuminated cameras, which resulted in well scanning starting at the bottom left well instead of the
top left. Now well scanning performs as expected - always from well #1 in the top left of the stage and
the well.

The CoolLED precisExcite LED light source controller has been improved and we can now offer direct
TTL control as well as USB to enable high performance switching. In addition we have removed the
need for the installation of the CoolLED supporting software (~100MB) so only the iQ installation is
required. Overall speed of acquisition has been improved by a factor of 2.

Recent changes to Sutter 10-3 filter wheel controller firmware had caused an error in communication
with iQ. We have now updated the Andor iQ adapter to fix the problem.

Andor laser combiner, ALC-401 controller has been improved to return actual power from Cobolt lasers.
The previous versions returned only the set power value. This is useful for monitoring performance. In
addition we have now ensured that all analog settings for unused laser lines are set to zero to minimise
any potential AOTF cross-talk.
Andor iQ Release Notes


Andor iQ 1.9 and iQ2-Py
             th
October 13 2008

Introduction and highlights

iQ 1.9 is intended to be our last release before iQ 2.0 which is planned for beta in late October. Version
2.0 has been in planning for some considerable time and we hope it will resolve many outstanding
issues with iQ 1.X. In particular we have been making iQ 2.0 scriptable with Python (www.python.org)
the widely used open source scripting language that is popular in scientific, web and even games
programming. We will refer to iQ 2.0 as iQ2-Py in future.

Some other key features which iQ2-Py will address are listed here.

         Threading and control limitations of the acquisition functionality of version 1.X.
         Simplified the GUI - removed the Protocol Wizard. Instead the user creates sub-protocols
         (timed channel acquisitions) which can be linked together into a master protocol for more
         flexibility.
         Parallel device communications will ensure that we achieve improved acquisition performance,
         essentially implementing each sub-protocol in an FLZ mode, but with Channels for flexibility.
         For the ultimate control, Python will allow initially direct sequencing of channels and FRAPP
         actions and in subsequent version it will allow direct control of individual device attributes.
         iQ-2Py will allow control of multiple cameras (and other devices) in one instance of the
         software, simplifying control and management of those systems.
         All graphics rendering will be implemented in OpenGL for performance and compatibility. Multi-
         pane Image windows will allow an image to be viewed by individual channels in a single
         window and MIP view is switched on or off by a checkbox click.

Python not only provides a Scripting framework for iQ2-Py, but also opens a rich world of open source
scientific programming to our users. With applications such as NumPy (Numerical analysis tools) and
the SciPy Scientific Python extensions (www.scipy.org) , users will have much more freedom to develop
extensions and take control of their data as never before. There are literally hundreds of extensions for
everything from graphical presentation (matplotlib, Chaco), to molecular modelling and even parallel
computing (http://www.parallelpython.com/) available and under active development. We look forward to
an exciting new era of open computing with iQ2-Py.



New features in iQ 1.9

FRAPPA – software support was improved in version 1.8.1 and first made available in version 1.8.
Once again we have improved its functionality by enabling multi-region bleaching both live and within a
protocol. Multi-region FRAPPA is a right mouse menu item on the Image Window and is toggled on/off.
When selected all regions will be bleached or activated, when off only the selected region will be
bleached. To enable the mode of baseline collection followed by FRAPPA action and then recovery
(classic FRAP) the user must Select a FRAPPA region. When no region is Selected the imaging
Protocol continues uninterrupted. So the user can now decide at which times FRAPPA action should be
initiated and whether all or just one region is bleached or activated.

FRAPPA is now available in Fast Protocols – but mouse down does block the sequence. iQ 2 will
extend multithreading to avoid this issue.

FRAPPA has been made independent of the PCU-100 series controller and now provides its own
Blanking signal to the ALC Laser combiner.
Andor iQ Release Notes



FRAPPA Calibration Wizard now stores multiple calibration files for different hardware configurations.

Andor Revolution CSU-X1, FRAPPA, TIRFM solution is an example of a system requiring distinct
FRAPPA Calibrations. Built on an IX81 microscope, our optical solution allows FRAPPA to be used
with either CSUX or TIRFM. The CSUX detector is used on the left port, while the TIRFM detector is
mounted on the right hand port. With a custom dichroic for the right port mirror FRAPPA can be used in
combination with TIRFM illumination and detection. However, because the detection paths are
dissimilar the FRAPPA angle to pixel mapping (Calibration) each must be stored in its own file.

The ImageList sorting bug has been fixed. You can now sort correctly by date, time, name etc.

A new Filter PlugIn is released with iQ 1.9 providing a range of 3x3 convolution and ranking filters.
These included high and low pass and morphological filters - close (minimum), dilate (maximum) and
noise removal (median)

Multi-Field ZDC and PFS capability has been added to the Scan control. One offset value is used for
all fields.

ALC/AOTF controller has been enhanced to allow 0.1% laser power control and capacity for 5 solid
state laser lines – see the ALC-501 series. Support for a new 594 nm laser line is now included.

CoolLED PrecisExcite LED source is now available globally from Andor and its distributors. It
integrated into iQ and is available in a bundle configuration with Luca-S or Luca-R and workstation.

Device Setup – the Record function has been simplified by removing the drop-down list and providing
a separate New button. On clicking Record the current channel settings are updated with those in the
current device control panels.

CSU-X1 filter wheel speed control has been added to allow vibration reduction in sensitive imaging
experiments.

Enhancements and bug fixes
Improvements have been made to the Olympus IX81, Nikon T2000E and TiE, TILL iMIC
microscopes and the Marzhauser stage drivers.

The Z drift problem when using Nikon PFS in time-lapse and FLZ has been fixed.
Andor iQ Release Notes


New features in iQ 1.8.1
          th
March 13 2008

Introduction and highlights

FRAPPA – software support was released first with version 1.8 and as expected in the course of
intensive use with the new FRAPPA hardware, we have learned from experience and in the current
release provide many enhancements to performance, including:

        FRAPPing of points and rectangles has been made more robust and we have added the ability
        to FRAP polygons with up to 10 vertices, extending the flexibility substantially. This includes
        both convex and concave polygons. In a future version we will increase the number of vertices.
        The FRAPPA Calibration Wizard which maps image pixels to FRAPPA galvo angles has been
        enhanced to allow easy store and recall of multiple calibrations for different imaging port
        configurations e.g. confocal vs. TIRF or widefield. This will also prove useful for calibrating
        different objectives whose optical centers are always slightly different.
        The FRAPPA channel should control only the laser combiner and FRAPPA unit. In version
        1.8.1 the FRAPPA channel can now be changed and “Recorded” from the Device Setup panel
        and maintain correct operation. This ensures switching time between FRAPPing and imaging is
        minimized.
        To ensure minimal “overspill” of region or point FRAPPing note that the active blanking
        connections communicated in the 1.8 release note must be used. See the figure reproduced
        below again to emphasize this point.
        Two bugs in rectangle operations have been fixed to ensure correct illumination time (multi-
        scan frequency calculation) and robust operation (a time-out error).




iXon FLZ improvements – FLZ control of the Yokogawa CSUX emission filter wheel has been added
to the controller, ensuring optimal performance with the CSU-X. In addition some bugs from the recent
introduction of improved sequence control have been fixed ensuring not only speed, but also robust
operation!
Andor iQ Release Notes


Andor SDK - a new camera SDK version (2.80) is included in the 1.8.1 installation, which provides
enhanced camera support, especially for the new Luca R, mega pixel EMCCD for budget-sensitive
applications.

Prior ProScan II – Closed loop servo window control has been added to the ProScan controller. This
enables the user to increase the servo loop error limit and ensures that a stage will not get into an
oscillatory “hunting for zero” mode.

New Device Support …

Polytrope for MA-TIRF on iMIC – TILL’s microscope has been enhanced to include control of the
Polytrope module, which enables rapid switching between wide field and TIRF imaging. Polytrope also
enables control of multi-angle TIRF and when used with Andor’s iQ and laser combiner provides a
flexible multi-angle TIRF solution. As ever the iXon provides the most sensitive camera for TIRF
imaging applications.

CoolLED PrecisExcite – LED light sources are attracting a great deal of interest in the microscopy
community for reasons of longevity, safety and environmental protection. We will be distributing
CoolLED and have therefore it has been integrated with iQ. It is a highly recommended device with
excellent integration, perfr5omance and control, including the Pulsed mode used to minimize photo-
bleaching. http://www.coolled.com/precisexcite/index.html

Sigma KOKI XY stage

Bug Fixes…

IX81 and Leica DMX - the iQ Olympus and Leica controllers clashed with new CSUX controller
introduced in version 1.8. This gave rise to a “Port 61” error in channels, which has now been fixed.
We apologize for any inconvenience this may have caused.

Sutter L10-C – A bug in the Lambda10-C and 10-3 firmware has been identified and corrected in
collaboration with Sutter. The bug related to an incorrect reset pattern after loss of sync with filter
positions 6-10. New firmware version later than 2.20 fixes this problem. We have embarked on a
filter wheel replacement programme in cooperation with Sutter for all Sutter 10C and 10-3 wheels sold
by Andor. L10-B and L10-2 controllers are not affected. Please let us know if you have experienced this
problem – loss of sync between software and firmware position.

Orca ER/AG – A frame dropping problem with Hamamatsu Orca cameras has been tracked down to
the DCAM camera drivers from Hamamatsu. Downloading and installing the latest version from
www.dcam.com will address the problem for those customers running iQ with this camera.
Andor iQ Release Notes


New features in iQ 1.8

                 Benefits for Revolution Systems and All iQ Users
           th
October 4 2007

Introduction and highlights

Multi-threading – Andor iQ core and Plug Ins already use multiple threads to enhance performance
and user control. As multi-core processors become the norm we continue to incrementally enhance all
parts of iQ to take advantage of the inherent parallelism of these processors. iQ 1.8 continues this
theme and many of the new components announced here have been optimized for this operation.

New FRAPPA - Exciting new possibilities in confocal, TIR and wide field live cell imaging are made
possible with the launch of Andor’s FRAPPA laser photo-bleach and activation unit. FRAPPA is an XY
galvo scan unit which delivers intense laser power to user-defined points, lines and ROIs for localized
optical stimulation. Andor iQ 1.8 provides an easy to use, integrated control and GUI for FRAPPA.
Modes of operation include (see www.andor.com for more information)
          Fast “point and shoot” mode for on-demand point and region Photobleach and Activation
          control. Switching time <=10 ms.
          Insert new FRAPPA keyword into Protocols enables controlled bleach or activation in
          sequences for applications such as FLIP.

Andor iCam – New firmware for Andor iXon and Luca cameras was recently introduced (see
www.andor.com), to provide significant improvements for multi-channel Live Cell imaging. iCam enables
key camera settings (especially exposure time) to be dynamically adjusted and implements fast
software triggers to achieve industry-leading frame rates. iQ 1.8 fully supports iCam capabilities and
many iXon cameras can be field upgraded to enjoy these performance benefits. A CCI-23 controller
card is required. Please contact your local representative for more details.

iXon FLZ improvements - A new sequence control approach allows us to overlap Piezo-Z settling with
camera readout and simultaneously achieves enhanced frame rates and improved Z settling! In
addition a number of bug fixes have been made to provide best performance in multi-channel frame
averaging and precise interleaved bright-field frame capture. Please see the drawing at the end of the
iQ 1.8 release note indicating necessary connections for optimum performance of the new FLZ.
Additional cables may be needed, so please contact your local representative if you have
questions.

New RollingBall filter PlugIn has been developed for background correction prior to analysis. This
works especially well for punctate features (e.g. single molecule data, foci or adhesion points). The
background can be computed for each frame or for only the first frame and applied to all and the
background can be output for averaging or other processing in mathematical image processing tools.
This approach works well as a pre-processor for e.g. Tracking and Spot analysis.

FastMIP and 4DView improved GUI controls and robustness. Note that you may need to update the
video drivers supplied with your workstation graphics card for best performance and reliability. Check
the website of your graphics card supplier.

New Yokogawa CSUX1 – Andor will officially launch Yokogawa CSUX1 at the 2008 Neuroscience
meeting in San Diego. Andor iQ 1.8 now supports all features all CSU models. CSUX1 is a new
generation device whose highlights include enhanced illumination throughput and uniformity, user
accessible dichroic mirrors and options such as motorized transmitted light path switch, emission filter
wheel and second camera port and a high speed disk version which provides up to 10,000 rpm.
CSU-10 and 22 units, whose performance remains class-leading, are still available.
Andor iQ Release Notes


Autofocus improvements – iQ management of Autofocus has been improved to handle hardware
focus errors. On the rare occasions when an Autofocus device fails to find its target, iQ now returns to
the last correct Z position. This gives Autofocus the chance to try again in the next call and avoids
possible total loss of focus, making long-term time lapse imaging more reliable and robust. The
performance has been extensively tested with TIRF imaging, where focus stability is critical.

Tracker has improved GUI and Snap with overlay features. Maths PlugIns - enhanced with Windows
Message Processing during operations, making them more responsive to user input.

New Format Converter PlugIn – convert image bit depth formats and select normalization method.

New OME-TIFF import and export PlugIn – enhanced interoperability with OME compliant platforms.

New Cameras Supported

Andor Luca-R and iKon DU934 – iQ 1.8 provides support for the new Luc-R mega-pixel EMCCD
camera (8x8 um pixels) and iKon DU934, 1kx1k back-illuminated CCD (13x13 um pixels). Both cameras
operate on USB 2.0 interface standard, providing convenient and cost-effective acquisition platforms.

Photometrix Coolsnap series FW (Firewire 400B) – we recently released the iQ driver for this popular
range of CCD cameras based on the Sony ICX285 sensor. Drivers for other fire-wire and competitive
PCI products from Hamamatsu, PCO and Q-Imaging are also available.

New and Improved Device Controllers

Laser combiner support extended to allow support for more Cobolt lasers – now includes Calypso,
Jive and Fandango with powers up to 100 mW.

Sutter L10-3 – The Lambda10 range has been extended to include a 3 wheel, 2 shutter model, which is
now supported. This unit operates with Sutter Smart Shutter or Uniblitz devices.

TILL PolyChrome 5 from TILL now controlled via RS232 interface with optimized switching speed and
control of power and bandwidth. This new controller makes use of multi-tasking for excellent
performance gains.

iMIC modular microscope from TILL has also been enhanced use of multi-tasking to deliver new levels
of performance. The current controller includes support for a USB joystick for comfortable XY stage
motion control.

Olympus IX81/BX61 controller has been improved to minimize overheads associated with
communications. This combined with internal buffering of motorized component settings delivers frame
rates of twice those of the previous controller.

Nikon TE2000E control now includes previously missing transmitted light control and switch. PFS
interface has been enhanced to allow continuous operation where the user requires it.

Leica 60000/4000 control has been improved to avoid recoding unnecessary settings during Channel
set up.



Third Party and Open Source Platform Compatibility Update

One of our goals is to continually enhance iQ data compatibility with established and evolving image
analysis and processing platforms. With this in mind we have an ongoing project to work with other
Andor iQ Release Notes


suppliers in the scientific field (including microscopy) and also to engage with research community-
driven open source projects to ensure data exchange and mutual file format support.

Bitplane, AG creators of Imaris have implemented an importer for our multi-TIFF format, further
enhancing cross-platform capabilities between our products. Thanks Bitplane! http://www.bitplane.com

Image-J We thank the team at UWI, Madison for implementing Andor multi-TIFF support within their
Bio-formats library. Bio-formats is available in various forms including a plug in for ImageJ open source
software. http://www.loci.wisc.edu/ome/formats.html

Micro-Manager – Our thanks to Nenad Amodaj and Nico Stuurman at UCSF for their work to support
Andor iXon cameras. Our software team has contributed a new component to their open source
acquisition Platform for Image J and we now maintain iXon driver support. http://ww.micro-manager.org

New OME-TIFF import and export PlugIn – enhanced interoperability with OME compliant platforms.
http://www.ome.org


Significant Bug Fixes

         Possibility of identical channel labels has been removed. This bug had the serious side-effect
         that once the channel are locked in acquisitions, the data had to be split and re-imported to
         change the labels. Identical labels makes channel analysis e.g. Ratio impossible to complete.
         Problems of crashes in Live mode with Field Split PlugIn have been resolved and
         enhancements to the flexibility have been introduced.
         Some FLZ bugs relating to multi-channel mixing while frame averaging have been fixed.
Andor iQ Release Notes


                           Release Note History Follows……..

                                     New features in iQ 1.7
                                                      th
                                             June 4 2007

Introduction and highlights
Major new features in iQ 1.7 include the following:

         Support for hardware Autofocus systems from ASI, Nikon and Olympus. A new keyword can
         be added to the Protocol, either at the first page of the Wizard or later with a right mouse click
         at the Repeat keyword. Autofocus control operates in both time-lapse and FastLZ.
         A new OpenGL FastMIP and 4D visualization Plug In enables real-time interactive volume
         rendering, by making use of advanced graphics hardware capabilities of graphics engines such
         as NVIDIA and ATI-Fire.
         Improved control of iXon with Andor’s new camera firmware included with the latest SDK. In
         FLZ new features include exposure control with wavelength, bright field image capture
         interleaved with scans.
         In time-lapse operation the new software trigger mode increases variable exposure frame rate
         up by a factor of between 2 and 5! Note that in order to take advantage of the new camera
         control a firmware update is needed, which can only be performed on cameras from serial
         number 2020 and requires the use of a CCI-23 controller card.


The “Autofocus (n, on)” keyword indicates that a hardware Autofocus action will be executed at the
start of the acquisition sequence loop. The value (n) is a loop count parameter and specifies the
frequency of the Autofocus action. If n =1, then Autofocus is executed on every loop, if n=2 then the
action is on every other loop and so on.

Each implementation has its advantages depending on the application.
        ASI CRIFF relies on an IR laser diode and TIR at the cover slip-specimen/medium interface. It
        is a continuous feedback system integrated with a piezo Z stage or ASI controlled Z stepper. It
        can be left on during single Z series (time-lapse or fast mode). For Z scans it can be left on
        during time-lapse intervals and automatically switched off before a Z scan is executed. One of
        its main advantages is that is can be adapted to most microscope models.
        Olympus ZDC is primarily a one-shot system, taking about 800 ms to execute a “find”
        operation. It relies on detecting the reflection signal from an IR laser diode at the cover slip-
        specimen interface and in iQ we record an offset to be applied to the focus position found to
        remain at the optimal user-defined focus plane. The one-shot mode is executed by the
        Protocol based on the Autofocus command settings and this makes it suitable mainly for time-
        lapse and Z scan operations. It is a robust system, which can be retrofit but is compatible only
        with Olympus IX81 microscopes.
        Nikon PFS (perfect focus system) is a continuous Autofocus system, which can be integrated
        with only the most recent Nikon TE2000 microscopes. Because of its continuous operation and
        short cycle time it is more akin to the ASICRIFF and can be used in all modes of operation,
        time-lapse, fast time and Z Scans.

Absolute stage coordinates have been improved to avoid Z calibration if not required. Multi-field
acquisitions, we introduced the MoveTo function on the Image Window right mouse menu to allow the
stage to return to the coordinate on the image. This has now been extended to Single field images
captured by Snap and Protocol execution.

New or Enhanced PlugIn functionality
Andor iQ Release Notes


The 3DView PlugIn remains, but we have added 2 new visualization PlugIns. These use Cg and
OpenGL programming to provide real time rendering of multi-dimensional data. FastMIP has been
especially prepared to enhance data review during a time-lapse or FastLZ experiment and making use
of Hyper Threading technology. Rendering quality is significantly enhanced using interpolation
techniques for both z-series and zoom functions. Movie animation and 4DView provide rendering speed
of approximately 10X faster and will benefit directly from advances in OpenGL compatible graphic
cards!

Tracker has been converted to an iQ PlugIn instead of a stand alone program. A number of bug fixes
and enhancements have been made to this module, including a new tracking method. Including it as a
PlugIn ensures that licensed users downloading iQ are assured of maintaining latest functionality. We
will release a further enhanced Tracker later this year.

Dual ImageDisk PlugIn allows data from two PC’s to be merged. This technique is used with two
camera systems, where the cameras are externally synchronized so that optimal frame-rates can be
maintained. This PlugIn allows alignment of the data sets during merge of the two data streams. The
alignment parameters are setup in the new Field Split PlugIn, described in point 6) below.

Camera Alignment PlugIn enables precise mechanical alignment of dual camera systems. The PlugIn
operates in either feature-matching mode or in overlay mode. In the former punctate features are
identified in the specimen and iQ segments and computes their center of gravities, reporting their
positions in XY and angle between the two. The user must align one camera to match the XY and
angle between the two spots on both cameras. Multi-spectral beads visible in both channels should be
used for alignment and it is advised that one camera should be flipped for the alignment to take into
account the optical flip in the dichroic or polarization splitter assembly included in our Dual Port Camera
Adapter.
In the overlay mode an image of one camera is captured and then accessed via the dual imagedisk to
be shown as a static image which is overlaid with the Live image from the second camera. Interactive
tools allow for image alignment.

Field Split PlugIn generates offset data for aligning either dual camera data (see 6 above) or field
splitting devices such as Optosplit II, III, DualView or QuadView. Support for 2, 3 and 4 split ROIs on the
same camera is supported. Improvements in both static and Live differential and overlay alignment have
been made and rotation control is now available, making the PlugIn more robust and easier to use.

Image Math and Image-Image Math PlugIns have improved image naming convention.


New and Enhanced Device Controllers

FastLZ iXon driver –
        i) Now allows for phase/DIC image to be taken in each sequence. Z position can be set –
        single frame taken at Z position.
        ii) Bug fixes in Ext Start selection and delay at Start of sequence with 860.
        iii) FastLZ with frame transfer (FT) option, enables performance benefit of FT when used with
        external hardware trigger generator (ET). ET must produce consistent interval between trigger
        pulses as pulse interval sets the exposure time in this mode.

TILL iMIC - New support for the modular automated microscope provides control of all parameters
including XYZ stage and piezo, objective turret, filter cube changers, bright field LED. A joystick control
for the iMIC XY stage is now supported in iQ from any Windows compatible joystick. The control
provides proportional control, with options on 3 maximum speeds – Slow = 1mm/s; Med = 5mm/s; Fast
= 10 mm/s.
Andor iQ Release Notes


TILL Polychrome V enhanced support via RS232 mode as well the previous analog mode. This
enables control of power and bandwidth settings as well as internal shutter.

Leica DM4000/6000 and DMI6000 microscope control has been completed with support from Leica. All
motorized functions from this new generation microscope from Leica can now be accessed and
controlled from iQ 1.7. We have also included control for the Leica Macro Fluor Zoom microscope and
have supplied a Revolution system to operate on this powerful large specimen fluorescence instrument,

Nikon TE2000 microscope controller has been developed with support from Nikon Instruments US.
The new controller supports all motorized functions on the instrument, including port switching, DIC
analyzer slider and the Nikon Perfect Focus system. We will extend control to the Eclipse i-series
upright microscopes in the near future.

Prior controller has been updated to allow for closed loop and open loop selection. Prior’s Lumen is
also supported in iQ 1.7.

Marzhauser controller has been improved to allow for closed loop and open loop selection. In common
with all stage controllers, the unit now auto-calibrates on iQ startup or before a scan is executed.

Enhanced Generic Shutter device now supports RS232 control of Uniblitz VM series controller as well
as LPT port output on suitable PC’s.

Improved Laser combiner operation is supported in iQ 1.7. This includes Active Blanking for absolutely
minimized specimen exposure. International Laser safety requirements have been complied with
using a new ALC driver which indicates when laser emission from the ALC is active.

Support for multiple XY and Z stages has been added. iQ allows the user to select the device to be
used for a scan. This is implemented to allow use of stepper plus piezo stages.

Some significant bug fixes

        The Channel DeltaZ bug has been fixed – it was not being operated correctly.
        Kymograph Access Violation on Delete All has been fixed.
        Montage Access Violation when launched from Protocol has been fixed.
Andor iQ Release Notes




                                 Andor iQ Release notes version 1.6

                                               November 2006

KIDAndorLZRTA
Prior filter wheel support has been added to FLZ mode. This enhances upgrade performance of Perkin
Elmer RS systems.
Till Polychrome monochromator support has been added to FLZ to enable optimum support for fast
imaging. Andor recommends the TILL monochromator as a fast, bright, flexible and quiet optical source.

Andor SDK
In dual iXon systems there was an initialization problem in FLZ mode, which has been fixed with the
release of SDK 2.76, included in this version of iQ 1.6.
SDK 2.76 also improves Luca performance regarding time out in Live issue.
One other occasional time-out error problem has been tracked to IRQ sharing. If this is a repeatable
problem we recommend moving the CCI card to a new PCI Slot.

Yokagawa
CSU21 support bugs have been fixed and CSU21 can be selected in the device settings tab. Note the
CSU21 requires a delay of a second or two to change and stabilize speed.
In CSU22 we have added an option to control DM and EM/BA filters separately, allowing more flexible
operation. The filters can also be “Linked” to enable the original mode, where the 3 are changed
together.

ALC - Andor Laser Combiner
The ALC was discovered to have a limiting effect on speed in fast imaging, due to a counter-timer error.
This has been fixed and now allows much higher frame rates in FLZ mode with binned, short exposure
imaging.

ASI stage support
Absolute stage coordinates have been added to the ASI controller to allow correct control and Montage
scan capability. We have also disabled front panel buttons to avoid e.g arbitrary Zero setting which is in
conflict with an absolute coordinate system.

Cairn mono
A problem with support for grating density-setting 2000 has been fixed.

Olympus Scope
Improvements have been made to the operation with the IX81 and BX61 microscopes. A stage interface
has been added to allow z to be disabled – e.g. if in use with a piezo for Z scanning or if motorized parts
have been added to an IX71, which does not include Olympus Z drive, but third party stepper. Motorized
switching the bottom port has been implemented. The new IX/BX controller uses the latest Olympus
SDK (July 04) for control.

Other bug fixes.



                          Andor iQ 1.5 Release Notes and Plans
Andor iQ Release Notes


                                               July 2006
1. New features

IQ 1.5 follows quickly on the heels of 1.4 and 1.4..1 and 1.4.2. This version will fix the issues created by
conversion to absolute stage coordinates and provide some significant improvements. We expect this to
be the last release before version 2.0, which is planned for launch at ASCB in December. The following
is a list of main features added to iQ in version 1.5 – no special order.

Multi-camera support - imaging systems with more than one modality e.g. TIRF and CSU. This allows
the user to register more than one iXon camera in a single instance of iQ and the user can specify
which camera will be used in a Protocol. Cameras must be used sequentially, not simultaneously. The
keyword Camera Selection is used in the Protocol.

Simultaneous dual-camera support - requires two PC systems, one acting as master. Using the
master to provide external triggers the cameras can be synchronised to within 2 microseconds and we
can supply an iQ PlugIn (runs on master) to merge data from the two PCs. We now manufacture dual
C-mount camera adapters for two wavelength imaging.

New FastLZ capabilities:
       Andor Laser Combiners – support for external laser combiners e.g. UltraView upgrades. This
       allows control of up to 5 laser lines.
       Sync bug and scrolling – a bug in SDK 2.75.0.0 has been addressed in this release (2.75.0.5
       included in the installation). Scrolling and sync Issues between DV885 and CCI-22 resolved.

ImageView – control for Image Zooming has been enhanced, providing independent Zoom in and
Zoom out tools with a Zoom multiplier of sqrt (2). AutoZoom fits the image into the current Window size
and a User-Defined Zoom is available from a right mouse menu on the Image – Select Tool/User Def.

Image Mapping (Scaling) – responsiveness has been improved and Automap is switched off
automatically if the user tries to drag the cursors in the Mapping dialog.

Montage scanning has been extended to provide a Linear mode in which the user defines only start
and end point of the scan region and iQ fits a line of overlapping fields. This will be beneficial for those
imaging linear features in areas such as DNA combing. Montage can be used with Z-scanning and also
in Time lapse operation for studying large specimen 3D structure and/or development.

Montage View PlugIn has been improved to provide (optional) pixel matching algorithms, which
perform correlation matching between the overlapping regions of montage scans. The performance
(provided there is contrast available) is pixel perfect and the user can specify the stage precision
(defined in micron rms) so that the search area can be limited and speed optimized. Other options allow
a brightest overlay method to minimize image shading effects. Montage capability is available only to
users who have the iQ-MF (multi-field) option.

Stage Alignment - Wizard has been improved using enhanced search algorithms. This is important for
Multi-well and Montage imaging for correct results. Users of earlier versions of iQ (or AQM) will need
to redefine all scans to ensure correct operation.

Stage Registration - When iQ starts a stage registration step is needed to establish “Home” or stage
zero position – this now includes a focus step so a test slide is needed. Further warnings help to avoid
damage to expensive objectives.

Move To has been added to the Right Mouse menu on the image window, when the image showing
has been created with a Scan or Montage. iQ will take the stage back to the coordinates specified by
Andor iQ Release Notes


the mouse and when you go Live you will see the feature at that location on the current specimen. This
is possible now that absolute stage coordinates are used.

Adjust Focus– A right mouse click on the Scan position in the Protocol can be used to adjust the focus
of all fields in the scan. This is useful for correcting focus drift in a time lapse acquistion. To Adjust
Focus while a Protocol is running click on Live, then in the Protocol Tree expand the Scan and at any
field position right mouse click and select Adjust Focus from the pop-up menu. The system will move
there, you can adjust the Z range or position and then when you select Next iQ will exit the Wizard,
adjusting all Scan Z values by the offset. When you click back to Idle the system should rescan the
current time point from Field 1 and then continue. The Adjustment is rippled through all fields Z
positions, making it suitable for compensating instrument thermal drift.

File Manager – File handling has been enhanced, iQ now writes a *.txt file (same name as image)
containing image details when any Image is saved.

2. New devices drivers and hardware support

Olympus IX81 and BX61 - improvements to Olympus IX81/BX61 control OCX have been made,
making control of the microscope from iQ smoother and more robust. A new layout for the keypad has
been adopted in line with more recent documentation for default settings from Olympus, Tokyo.



                 Olympus IX81/BX61 Handset
       Epi              BF                                                          Esc

     FW3-           FW3+            FW2-           FW2+            FCT-            FCT+
                                                                                    =+
                                 OBJ2                  OBJ3
        OBJ1                                                                  OBJ4
           Ө
                         BtmPt                                OBJ5
                                           OBJ6

    Figure 1 New Olympus IX81/BX61 Handset control button actions while iQ is running.

    KEY:
       •     Epi – Toggle Epi Shutter
       •     BF – Toggle Bright Filed Shutter (if present)
       •     Esc – Escape – Drop Objective turret for safe change.
       •     FW3+/- – Filter wheel 3 increment and decrement (if available).
       •     FW2+/- – Filter wheel 2 increment and decrement (if available).
       •     FCT+/- – Filter cube turret increment and decrement (if available).
       •     OBJ 1…6 – select objective (turret position).
       •     BtmPt – Bottom emission port if present.
Andor iQ Release Notes


Physike Instrumente – PIFOC controller model E665 support has been improved, so that iQ can now
control the P721 and P725 objective positioners to provide 100 and 400 um travel respectively. This
module will also provide analog control to PI and other piezo devices such as Piezo-Jena and MadCity
Labs piezo Z stage.


3. Key Bugs fixed

         Acquisition calibration being applied to Image Window.
         Image scrolling at binning > 1. SDK 2.75.0.0 fix.


4. Forthcoming Patches and Plans for iQ 2.0

iHere are some of the things you can expect in forthcoming patches:
         New device support planned for Nikon LUSU – TIRFM laser illuminator.
         Leica DM-4000 and DMI-6000 driver.
         Tracker as an iQ PlugIn, with new features and bug fixes.
         Illumination “flat-field” correction to improve Montage rendering and segmentation for Spot
         analysis and Tracker.

Later this year we plan to issue iQ 2.0, which has a more modular architecture and provides SDKs for
Auxiliary Device driver development, as well as camera and PlugIn SDKs. We have already begun
work and plan improvements in 4D visualisation and analysis, which is core to Andor’s Revolution
confocal product range and multi-dimensional imaging in general.
Andor iQ Release Notes


                           Andor iQ 1.4 Release Notes and Plans
                                         May 2006
1. New features

The following is a list of main features added to iQ in version 1.4 – no special order.

Montage scanning allows iQ to capture images from a user defined region of the specimen and then to
“stitch” these together to create a high resolution view of that region. As scanning proceeds the focus
plane is adjusted from user-defined reference points to ensure optimal focus is maintained across the
whole scan. Montage can be used with Z-scanning and also in Time lapse operation for studying large
specimen 3D structure and/or development.

Montage View PlugIn implements the rendering or “stitching” and can be activated from the Protocol
Tree. Images created in this process can be viewed, analysed and processed like any other nDim in iQ.
Montage capability is available only to users who have the iQ-MF (multi-field) option.

Stage Alignment and Registration - a new Wizard has been added for those users with motorized
stages to ensure that camera and stage X,Y coordinates are collinear. This is important for Multi-well
and Montage imaging for correct results. Users of earlier versions of iQ (or AQM) will need to redefine
all scans to ensure correct operation and to take advantage of these new features. In addition Scan
users should note that we have now implemented absolute stage coordinates in iQ. This means that
you should be able to return to the same point on a specimen between sessions. It also means that
when iQ starts a stage registration step is required to establish the “Home” or zero position.

Calibration has been enhanced allowing a new “Automatic” mode. In this mode the user selects the
objectives available on their scope (along with any Optovar and/or C-mount magnifications) and then
selects the camera in use. The Calibration Manager then computes the effective pixel size for all
objectives lenses in a single step. Interactive calibration with a graticule or haemocytometer can still be
used. Predefined tables store microscope objective magnifications (and color codes) and camera pixel
sizes for ease of use.

Acquistion Calibration - applies the selected XY values to all data acquired from the camera(s) via the
Snap or Protocol execution.

Edit-Calibrate – allows you to calibrate the current (displayed) image from the list of calibrations
available. This process has been separated from acquistion calibration for clarity and to avoid
inadvertent changes in calibration, which were possible in the previous global calibration method..

Z-Scan – Z scans can now be adjusted each time the Protocol is run to adapt to varying sample depth.
Nyquist and Cubic voxel scan options have been added for the selected objective lens.

iXon driver and FastLZ – a major effort in this component delivers many new features including
enhanced GUI, extra trigger modes and support for components central to the Andor Revolution
confocal systems. Tips provide suggestions on how to improve performance when required.

New FastLZ capabilities:
       12, bit, Linear and Real EM gain supported for iXon+.
       Fastest - streams images into RAM to achieve maximum speed at frames greater than 50 fps.
       This proves very useful for sub-arrays and/or iXon 860 users achieving optimum frame rates.
       External Start – minimizes trigger to first frame delay in Fast Time protocol - delay. Requires
       TTL input to camera Ext Trig.
       Frame Averaging – Acquire images with average of 2 to 256 frames for SNR improvement.
       Exposure time control - GUI has been simplified.
Andor iQ Release Notes


         M x N Binning – independent X and Y settings with binning factor up to 16.
         Anti-ageing - time-out in Live mode.
         Ludl and Sutter - emission wheels in Fast LZ.
         Andor Laser Combiners – support for the Andor laser combiners (models 103, 104, 153, 401
         and 421) has been added to Fast LZ providing rapid shuttering and intensity control via the
         integral AOTF.
         Simultaneous multi-laser excitation – ALC control allows simultaneous selection of multiple
         laser lines..
         Go To Center Z – two new controls have been added to the Sequence tab - one goes to
         center of piezo range, the second goes to center of scan. Piezo range is now user-defined
         allowing support for the increasing range of devices in the market e.g. 100, 200, 460 um.
         External shutter control – enhanced in the Fast LZ Timing tab, with transition timing –
         suitable for Uniblitz and Smart Shutter drivers.
         TTL Input/Output Control - enhanced and extended in Fast LZ. A parallel thread monitors
         external events continuously, minimizing lost events.
         Sequence GUI – enhanced to support new devices and improve layout. The Lambda control
         has been improved to allow easy switching between different illumination/emission controls.
         Bugs - All known bugs have been fixed.

Episodic Averaging PlugIn
A number of episodes or sequences (commonly triggered to ensure precise time alignment) can be
averaged to improve SNR. Sequences are typically gathered with a recursive Protocol, using Load
Protocol to reload and generate a number of (near) identical episodes. The PlugIn also provides
Photobleach or baseline correction.

Kymograph PlugIn – Lamella Mode
A new “Lamella Mode” has been added to the PlugIn which is intended to ease the analysis of
lamellapodia protrusion and contraction rates in cell signalling, motility and membrane ruffling studies.
The new mode allows the user to draw a series of lines in the XY plane (or MIP) to create a set of
kymographs which can be further probed with the poly-line tool. The slope of each poly-line segment
delivers a protrusion or contraction rate which is reported into a data table, ready for export into a tab
delimited text file. This tool has been used by one of our beta site testers for several months and has
helped to deliver rapid and accurate analysis.

Time-lapse – Protocol length (duration) can now be set by time as well as frames. Elapsed time is now
reported during a protocol in the acquisition status panel.

File Manager – Fix to SIF file reader. Enhancement of Single TIFF file export to include time and other
dimension stamps, allowing reconstruction of data in third party software that cannot read/interpret ABD
multi-TIFF files.

Saving images with Overlays – Movie editor now allows a Save option to single 8/24 bit TIFFs and by
using the Stamp tool image parameters such as Time point, Z position etc can be burned into the
image. This allows transfer of data to 3rd part image analysis programs.

ImageList Save - options enhanced to allow multi-image export to single 8/24 bit TIFFs. Note that
ImageList details can be Copy/Pasted into text files as required.

Hot Keys – there is now one Hot Key Settings saved for each hardware Configuration.

Copy to Clipboard from Grids – Analysis, RGB and Spot tools now have a right mouse pop-up menu
to data from selected cells to be Copied to the Clipboard. The data can then be pasted into other
applications e.g. Excel.
Andor iQ Release Notes


Configuration Manager – the Local administrator restriction has been removed from configuration
manager. Now any user can create a Configuration. Changing global setting is still restricted to local
administrators to avoid inadvertent changes that will affect all users.

Power Out Protection – on receiving a shut down signal from Windows iQ now has a timed response
window to allow for closure on impending termination. This allows for a clean exit following UPS closure
in power outages.


2. New devices drivers and hardware support

Andor Luca - our entry point EMCCD camera is now supported under the iXon camera OCX.
iXon+ - New features for Andor’s flagship imaging camera including linear EM gain.

ALC-400 series – A new driver for the Andor multi-line solid state laser combiner provides control and
monitoring by iQ in both Time-Lapse and FLZ modes. An integral AOTF is used to provide microsecond
shuttering and intensity modulation via the PCU-100 series.

Ludl - 10 position filter wheels and triple shutter control is now supported. Speed improvements have
also been made. The new driver provides support for the MAC2000 legacy controller for filter wheels
and XYZ stages.
NOTE: When using both the MAC5000 and 2000 controllers the Z motor address must be set to “6” on
the Z controller card.




                 Olympus IX81/BX61 Handset
       Epi             Port                                                         BF

        F1             F2             F3              F4             F5             F6

                                 OBJ+                    NA
         OBJ-                                                                  NA
           Ө
                            NA                                  NA
                                             NA

    Figure 1 Olympus IX81/BX61 Handset control button actions while iQ is running.

    KEY:
       •     Epi – Toggle epi-fluorescence shutter.
       •     Port – Switch emission port – side, ocular, {bottom, right}.
       •     BF – Toggle bright-field shutter.
       •     F1…F6 – Select fluorescence turret filter position (1..6).
       •     OBJ Ө - Decrement objective turret position i.e. current -1.
       •     OBJ - Increment objective turret position i.e. current +1.
Andor iQ Release Notes



Olympus IX81 and BX61 – GUI and control improvement - iQ now controls the transmitted light on/off if
no shutter is available. Handset control enabled while iQ connected to microscope – for HS button
assignment see Figure 1 above.

Physike Instrumente – PIFOC controller model E665 support has been improved, so that iQ can now
control the P721 and P725 objective positioners to provide 100 and 460 um travel respectively.

Sutter DG5 – the DG4 driver has been extended to support the DG5 in RS232 control and to handle the
Smart Shutter as a stand alone device.

Sutter - Smart Shutter – confirmed functional via RS232 control using both DG4/5 and Lambda-10 FW
drivers. If a stand alone Smart Shutter is used with a Lambda 10-2 for example, then the DG4 driver is
loaded and the Smart Shutter Device is selected on the Settings tab.

Yokogawa CSU – the CSU22 driver has been enhanced to ensure correct synchronisation between the
GUI and the device. A CSU10 control option has been added which enables the shutter to be controlled
from a PC LPT1 (parallel) port.

3. Key Bugs fixed

         Random vcl40 canvas error in exposures >= 1s.
         Zero default baud rate for PIFOC E665 controller.
         Frame orientation error in Snap FLZ.
         Shutter opening too early in Fast Time series.
         Movie Editor saving with Overlay error.
         Overwrite of existing movie file fixed.
         Abort in Image Allocation breaks subsequent Live or Snap.
         Fix to SIF file reader to allow loading of sequences from MCD/Solis up to 2GB.
         Demo mode start up error.
         Multiple Save from ImageList “Delete after Successful Save” response options.
         Spot threshold and feature delete bugs.
         Shutter opens too early in “Pause”, “Delay” or “Trigger In” to Start.
         Events are now cleared after a Protocol has been completed.
         Shut down Chart 50 error.


4. Forthcoming Patches and Plans for iQ 2.0

As with all software projects, there is no end to the possibilities, but at some point we have to call a halt
and make a release. Thus iQ 1.4 delivers much, but leaves more to do. Here are some of the things you
can expect in forthcoming patches:
         Leica DM-4000 and DMI-6000 driver.
         Tracker to be an iQ PlugIn, with new features and bug fixes.
         Illumination “flat-field” correction to improve Montage rendering and segmentation for Spot
         analysis and Tracker.
         Multi-camera support for imaging systems with more than one modality e.g. TIRF and CSU.

Later this year we plan to issue iQ 2.0, which has a more modular architecture and provides SDKs for
Auxiliary Device driver development, as well as camera and PlugIn SDKs. We have already begun
work and plan improvements in 4D visualisation and analysis, which is core to Andor’s Revolution
confocal product range and multi-dimensional imaging in general.
Andor iQ Release Notes


                         Andor iQ Release notes version 1.3

                                         November 2005


Installation Improvements

In previous installations three steps were required for the three software components – Andor
iQ, PCI card driver and iXon camera driver. In the current release these steps have been
integrated into a single iQ installation with the latest Andor SDK 2.73 included. This should
make download and deployment simpler and faster. This version will appear on ftp.andoriq.com
for download by Friday November 11th.

Summary of Software Improvements

    Andor iQ.exe
    Fixed Standard Deviation bug in Thru Series analysis. Increase number of fields in user
    defined scans from 99 to 9999 fields. Improved Device Setup dialog for New Channel.
    Fixed on-line ratio bug. About box reflects Andor iQ release version (as well as build
    number and date).
    Andor FLZ.ocx
    Wavelength support extended to DG4, Cairn and Kinetic Monochromator and AOTF.
    Improved performances regarding speed, synchronization and user interface.
    Ki001comp.bpl
    Decouple display and acquisition for flexibility using messaging. Also allow the display
    update message to monitor the pixel value under the cursor. Improvements to Scale bar,
    other annotations and ROI operations including Paste and Default settings.
    mm40.dll
    Speed up image allocation for long sequence acquisition. Fix to Abort button - now
    terminates image allocation. Increase Image XY size limit from 4kx4k to allow up to 2GB
    per frame. Remove 2GB warning message.
    fm40.dll
    Fixed bug in Andor SIF file loading. Set 2GB limit on SIF file load.
    AOTFcontroller.ocx
    Support AOTF control for both Fast LZ and standard Time Series. This supports Andor’s
    laser combiner products (requires PCB 100 series) and some 3rd party AOTFs.
    Lvpzt.ocx
    Support for Physike Instrumente PIFOC devices extended to E665 as well as E662
    controllers. In addition to RS232 both now have a direct voltage control mode (DAC).
    Cairnmono.ocx
    Cairn Research OptoScan is now support under our standard card PCIM-DDA06/16 MC
    DAC board in both FastLZ and Time Series mode. Continued support DT331.
    Priorcontroller.ocx
    Clean up of user interface.

				
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