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Revision as of 06:25, 5 August 2011

Summary: Interfaces with Andor cameras
Authors: Nenad Amodaj (Windows)
Karl Bellvé (Linux port)
Jizhen Zhao, Daigang Wen, Francis McCloy (Andor contributors)
Maintainers: David Gault (Andor)
Arthur Edelstein
Karl Bellvé (Linux port)
Pariksheet Nanda (Andor) this document
License: BSD
Platforms: Windows and Linux (No Mac driver available)
Devices: iXon/iXon+
Luca-S, Luca-R
Clara

Installation

Andor SDK

You must install the Andor SDK, or Andor camera application software (Solis or iQ), since it contains the necessary files to recognize the camera. If you need to download a copy of the Andor SDK, since is not publicly available, request Andor support to gain access to it, stating in the support request form you need the drivers for µManager.

Disable power savings

Commercial computers like Dell, HP, etc shipped in the US and Europe are legally required by environmental regulations to ship with all power savings turned on. These must be disabled in the BIOS.

Additionally for Windows 7, turn off PCI power management and USB suspend settings

Test communication

The Andor SDK installs test programs that can be used to get live images:

     C:\Program Files\Andor SOLIS\Drivers\Examples\C\

Identifying computer bus speed bottlenecks:

  1. iXon PCIe cameras can have their live stream stops after 2 or 3 images or not start at all. The reason is PC motherboards throttle the PCIe speed depending on the daughter boards populated. Make sure you plug the PCIe card into a fast enough bus. For example the Dell XPS desktop 1x PCIe bus does not work with a PCIe 16x graphics card, so you have to connect the Andor PCIe card in the 8x PCIe slot instead
  2. USB cameras using high bandwidth such as the Clara must be plugged into the computer to be its own USB bus. On Linux you can easily check if this is the case with lsusb -t. On Windows you need to use a utility like UVCview ftp://ftp.efo.ru/pub/ftdichip/Utilities/UVCView.x86.exe. The Linux output below shows that the Clara (Vendor 0x136e Product 0x000e) has been correctly plugged into its own USB bus (Bus# 1):
     $ lsusb -t
     Bus#  5
     `-Dev#   1 Vendor 0x1d6b Product 0x0001
     Bus#  4
     `-Dev#   1 Vendor 0x1d6b Product 0x0001
       |-Dev#   2 Vendor 0x046d Product 0xc045
       `-Dev#   3 Vendor 0x2341 Product 0x0001
     Bus#  3
     `-Dev#   1 Vendor 0x1d6b Product 0x0001
       `-Dev#   2 Vendor 0x03f9 Product 0x0100
     Bus#  2
     `-Dev#   1 Vendor 0x1d6b Product 0x0001
     Bus#  1
     `-Dev#   1 Vendor 0x1d6b Product 0x0002
       `-Dev#   6 Vendor 0x136e Product 0x000e
     $ lsusb
     Bus 005 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
     Bus 004 Device 002: ID 046d:c045 Logitech, Inc. Optical Mouse
     Bus 004 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
     Bus 003 Device 002: ID 03f9:0100 KeyTronic Corp. Keyboard
     Bus 003 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
     Bus 002 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
     Bus 001 Device 006: ID 136e:000e  
     Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Using UVCview:
UVCview on Windows showing the Clara by itself on the USB bus

Device Configuration

  1. Open Micromanager.
  2. You will be prompted to load a configuration file. To create a new configuration file use "Tools" > "Hardware Configuration Wizard..." to manually add the device.


Device Settings

Set camera properties under "Tools" > "Device/Property Browser..." Micromanager does not offer every feature available in Andor Cameras. TODO: List camera features not available in Micro-Manager. However for the Clara overlap mode, Extended NIR and the variable pre amp gains are available.

Cooling

  • iXon cameras MUST be cooled to the specified temperature: at least -60 C for DV models and -70 C for DU models.
  • Offset ("Baseline") is optimal at this setting. If the camera is not cooled, the offset can be display as 0 data counts.
  • Some blemishes are compensated at the specified temperature setting and will be more visible at warmer temperatures.
  • No need to warm up cameras before shutdown of software and computer (since condensation does not occur).
  • Full gain will not be achievable without cooling.
  • EMgain is temperature compensated for RealGain cameras.
  • Clara must be cooled to the specified temperature: -45 C with fan, -15 C without

Electron Multiplying Gain (EM Gain)

EMgain range

  • EMgain does not start at 1 for all cameras. The start level is tuned for each EMCCD chip.
  • The actual EM gain range depends on the model of your camera: it can be from 0 to 255 (non-linear), 4096 (non-linear), or RealGain 1000 (linear)

EMgain slew rate

  • iXon, iXon+, Luca-R and Luca-S
  • EM gain levels should be kept same between channels during an acquisition (because EM gain levels should not be immediately switched)
  • EM gain circuitry is powered by a high +53V voltage rail and the gain applied to the EM readout register is proportional to this voltage.
  • Thus when you increase or decrease the EM gain on the camera, you have to wait for the voltage slew to stabilize at the new set value.
  • This is typically about 1-2 seconds, the maximum time being from setting EM gain from 0 to the maximum value of 1000.
  • Thus it is much better to vary exposure times or excitation signal intensity rather than switching EM gain levels in a multi-channel acquisition (unless you know what you are doing)

Pre-Amplifier Gain (PAG)

  • Pre-Amplifier Gain is a historical name since this feature predated EMCCD cameras. The "Pre-" is in relation to the Analog-to-Digital (A2D) convertor, so PAG refers to the opamp between the sensor and the A2D convertor.
Note: On EMCCDs it is confusing to talk of PAG since one may think this "pre-" amplification happens before EM gain amplification. However EM amplification happens on sensor, and PAG happens "post-" readout of your sensor.
  • PAG multipliers like 1x, 2x, 4x can vary between cameras since they are tuned for each sensor.
  • PAG can affect the saturation limit of your image. To determine the expected digital saturation limit, consult your camera performance sheet of your camera. Divide the "Saturation Signal per Pixel (Electrons/pixel)" by the "CCD Sensitivity (Electrons/A2D count)" to get saturation signal in digital counts.
Warning: Always set PAG to maximum when using EM gain. PAG is useful in Life Sciences only in Conventional mode

Conventional CCD or EM-CCD mode

  • With the exception of the 885, you can switch between CCD and EMCCD modes via the Output_Amplifier setting
  • EMCCD readout without EM gain is more noisy (~40e read noise) so Conventional readout (~6e read noise) is beneficial if light levels do not require EM gain.
  • Benefits of EM gain combating the EMCCD readout register noise of ~40e can be seen from 45x onward, i.e it is better to use 45x EM gain and upward.

iCam


Troubleshooting

iXon: PCI/PCIe card not found on Windows 2000/XP

If the iXon PCI/PCIe board is plugged in before you first install the

and plug in your camera and Windows tries to recognize it, choose:
   Install from a list or specific location (Advanced) >
   Search for the best driver in these locations >
   Include this location in the search >
   
   C:\Program Files\Andor SOLIS\Drivers\

Clara: error code 22

The camera cannot be seen because either the Andor SDK version is too old.

Andor introduced Clara support in their SDK v2.84

When trying to create a fresh configuration you may get error code 22, Andor error code 20006 (unable to load cof/rbf file). This is because your particular Clara needs file version >=2.87 because it has newer firmware.

In either case you need to copy the library file from your Andor installation to your Micro-Manager directory. If you have the Andor SDK, copy and overwrite:

     C:\Program Files\Andor SOLIS\Drivers\atmcd32d.dll

To:

     C:\Program Files\Micro-Manager-1.4\atmcd32d.dll

64-bit users should copy the library atmcd64d.dll instead

Clara: Java exception using Live, Overlap mode with Clara-Output_Amplifier in "Extended NIR" mode

This is a bug with the DeviceAdapter.

The camera hardware does not support Extended NIR with overlap; the option should not be populated in the drop-down list.


Resources

Development support

Please liaison with Micro-Manager developers to contact the Andor software team

Click here to search for Andor on the Micro-Manager mailing list archive.

Andor support

For contacting Andor product support regarding any questions, see under "Support" for your location - http://www.andor.com/contact_us/default.aspx

P.nanda 11:27, 30 July 2011 (PDT)

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