McClean: NikonTI-Eclipse Setup and operation using Micromanager

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This is the protocol for setting up the Nikon-TI microscope and attached systems for use with Micromanager, but can also be used as a general guide to setting up any system with Micromanager.

Contents

Hardware Setup

Before beginning any setup, it is important to determine exactly all of the different components of the system. Our system is composed of the following:

  • Nikon TI Eclipse Microscope with Perfect Focus System (Includes a lot of components but you only need to worry about the scope itself) More Details
  • Andor Zyla sCMOS Camera More Details
  • 2 Lambda SC SmartShutters and Controllers (1 for DIC and 1 for Fluorescence )More Details
  • Prior Lumen 200 Fluorescence Illumination System (Is not controlled directly by Micromanager, it's just a lamp)More Details
  • HP Workstation z420 64 bit Windows 7

Specific Hardware Configuration for the Andor Zyla Camera

The Andor Zyla camera is connected to the computer using a PCI express card x4 card. This card is normally installed in a PCI express x4 slot as it is supposed to be. However, it may need to be moved to a PCI express x8 or x16 slot not because of speed concerns but power issues. According to an Andor technician: "I believe that it might be due to some as yet unknown BIOS setting limiting the voltages to the x4 or lower PCI slots. It has become common practice to introduce energy saving modes into modern computers, and occasionally these can conflict with high performance devices. If we were to find the correct BIOS settings, it would be possible to use the x4 board instead." PCI Express Slot Examples

Additionally, the power saving settings in the Bios need to be changed for similar strange power requirement reasons. Specifically for HP computers, go into the bios (hit ESC on computer post screen then F10 to go to computer setup). Under the Power tab go to OS Power Management and change Idle Power Savings from Extended to Normal. Save and restart the computer. It is my general understanding that regardless of what motherboard/computer, it is best to turn off/reduce any OS or hardware related Power Savings functions in order for the Andor/Bitflow PCI board to operate effectively because they do not like the environment.

Installing Drivers

Before any of these devices can be interfaced with Micromanager, drivers must be installed so that Windows recognizes them. I would recommend doing a clean install of all the drivers. If you have a fresh copy of windows then you can proceed straight to installing the drivers. However, if there might already be drivers for any components already installed you should delete them (Technically this isn't necessary but sometimes you will run into the problem of drivers conflicting with each other).

Deleting Old Drivers

†If Nikon Software is installed, it is ok, but if you want to be super safe uninstall that too.

  1. Removing Programs through Control Panel - go to the Control Panel and then Remove Programs. Remove anything related to Andor (Andor Driver Pack, Andor SDK3), Lambda, and BitFlow (Bitflow is the company that makes the PCI express chip used by Andor; they provide their own software).
  1. Removing Drivers through Device Manager - go to Device Manager (Control Panel -> Device Manager). Under Imaging Devices if you see "Bitflow Neon", right click and Uninstall Drivers. Then under Ports, uninstall all Lambda SC devices. And under Universal Serial Bus Controllers, uninstall all Lambda SC devices.
  1. Cold reboot the computer. Meaning do not use the restart function, use the shutdown function and then manually press the power button. This clears the memory which prevents some hardware/driver related issues.
  1. After the computer restarts, go to Device Manager. Other than Nikon Ti (if you have it installed already), there should not be anything else installed.

Installing New Drivers

Remember to COLD reboot after EACH driver installation.

Nikon Ti

  1. Nikon Control and Nikon Drivers
  2. Cold reboot
  3. Go to Micromanager Device Site and download the latest SDK installer. I used 64-bit 4.4.1.714 Direct Link
  4. Cold reboot
  5. After installing one of these, you might need to tell Windows to use the new driver by opening the Windows Device Manager, finding the Nikon Ti microscope (under Imaging Devices), and choosing Properties from the right-click menu. Click Update Driver and tell Windows to search C:\Program Files\Nikon\Shared\Drivers (or the appropriate equivalent on your system). Note that the driver version number differs from the SDK and library (DLL) version numbers (the main DLL is normally installed at C:\Program Files\Nikon\Shared\Bin\NikonTi.dll). (Taken directly from Micromanager Device Site )
Testing Nikon Ti
  1. To check that everything is working, open Ti Control and make sure that you can control the objective turret and the filter turret.

Andor Zyla

In general, follow the instructions on this page Micromanager Andor Devices. (Don't worry about the Micromanager root directory stuff yet.)

  1. Install Andor Driver Pack 3 by going to Link. Create an account if you don't have one (it's free). Download Software -> Drivers and 3rd Party -> Andor Driver Pack 3.6.30003.0 (sCMOS). You might have a different version but make sure it is sCMOS.
  2. Cold reboot
Testing Andor Zyla
  1. Go to Device Manager and you should see Bitflow Neon under Imaging Devices. Bitflow should now also be installed. To test camera, use Andor Solis if you have it and it should allow you to take an image.

Sutter Lambda SC

  1. Download SI Lambda USB Driver from Sutter Website (I used V2.08.28)
  2. The Lambda drivers are not packaged in a nice executable.
  3. Connect and Turn on Shutters
  4. If Found New Hardware Wizard appears, select Install from a list or specific location and navigate to the unzipped SI Lambda USB Driver folder
  5. If the Wizard does not appear, go to Device Manager -> Ports. There should be something there called "Unknown" or something like that. Right click and go to Update Drivers and then select Install from a List or Specific Location and navigate to the unzipped SI Lambda USB Driver folder
  6. You just installed the Serial port drivers but not the USB ones yet.
  7. Cold reboot
  8. If Found New Hardware Wizard appears again, select Install from a list or specific location and navigate to the unzipped SI Lambda USB Driver folder
  9. If the Wizard does not appear, go to Device Manager -> Universal Serial Bus Controllers. There should be something there called "Unknown" or something like that. Right click and go to Update Drivers and then select Install from a List or Specific Location and navigate to the unzipped SI Lambda USB Driver folder
  10. You have now installed the USB drivers
  11. Cold reboot
  12. Go to Sutter Install Instructions if any of this was unclear. They have a slightly more outdated but more detailed set of instructions.
Testing Sutter Lambda SC
  1. Go to Device Manager. Under Ports you should see Sutter Instruments Lambda (COM ?). Under Universal Serial Bus Controllers you should see Sutter Instruments Lambda. If you have both Lambda SC controllers connected you should see two entries in each. Remember the COM port designations for each of them, they should be different. Mine were COM 4 and COM 5.
  2. Download Lambda Test from Sutter Website
  3. Open Lambda Test (Lamtest.exe) in the unzipped Lambda_Test folder
  4. Following is adapted from ReadMe_Lambda_test.docx
    1. Set COM Port to the COM port designation of one of the controllers.
    2. Set USB Baud Rate to 128,000 for the controllers we have
    3. Click Open Com (The readout panel should indicate the the COM port was successfully opened)
    4. Under the Shutter Controls tab, you should now be able to control the shutter by clicking openA or closeA
    5. Once confirmed, Close Com
    6. Repeat with other COM port dosignation for the other controller.
  5. Close Coms and close the Lamtest (Make sure to Close Coms otherwise Micromanager might not see the controller since it is in use by Lamtest)
  6. Cold reboot just to be safe

Micromanager

Read This User Guide and This Configuration Guide

Installing Micromanager

  1. Install the latest nightly build found here (64bit version)
  2. Go to C:\Program Files\Andor Driver Pack 3\ and copy the following 3 files to the Micromanager root directory (most likely C:\Program Files\Micromanager )
    1. atcore.dll
    2. atdevregcam.dll
    3. actl_bitflow.dll

Configuring Micromanager

  1. Following the instructions of the Configuration Guide
  2. When you get to step 2, Add or Remove Devices, add the following:
    1. AndorSDK3 -> Andor sCMOS Camera | Andor SDK3 Device Adapter
    2. NikonTI -> TIScope | Nikon TI microscope
      1. TINosePice
      2. TIFilterBlock1
      3. TIZDrive
      4. TIXYDrive
      5. TIPFSOffset
      6. TIPFSStatus
      7. TILightPath
      8. TIAnalyzer
    3. SutterLambda -> Shutter-A 10-2 | Lambda 10-2 shutter A
      1. After clicking add, choose the desired COM port
      2. Then in the Port Properties window change the BaudRate to 128,000
      3. Repeat with different COM port for the other shutter
  3. In step 3, set Default Camera to Andor, Default Shutter to DIC, Default Focus Stage to TIPFSOffset and check Auto-shutter
  4. In step 4, give TIFilterBlock1 a delay of 250 ms because : " In our experience, movement of the dichroic turret (Filter Block Cassette) causes significant vibrations in the microscope. This results in blurry images. To avoid this, add a delay (step 4 of the hardware configuration wizard) to the FilterBlock device. A delay of 250 msec seems to work well." (from Micromanager Documentation)
  5. In step 5 label everything accordingly (you can always go back and change this later)
  6. In step 6 Save.
  7. Check that you can control each shutter manually
  8. Check that you can snap an image
  9. Check that you can set XY points

Rejoice

and Cold reboot again

Notes

  • Sometimes, the camera does not get recognized for some reason. Best way to fix this as far as I know is to restart the computer and the camera. Just restarting Micromanager does not seem to fix it. Still working on this bug.
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