BX Microscope, Arduino shutter and Micro-Manager

https://sils.fnwi.uva.nl/bcb/BX_2016/MD/bx_installation.html

First-time installation

N. Vischer, 08-Feb-2017

see also: BX-macros and download

A combination of the following hardware and software components is currently used for our BX microscope. Since 2016, the configuration was changed so it operates with a Hamamatsu camera (USB3), the newest version of Micro-Manager, and a Dell PC (Windows 7).

Hardware:

• Olympus BX microscope
• electromechanical UV shutter
• Shutter box with Arduino Uno microcontroller and USB

Old setup:

• Coolsnap fx camera (Roper Scientific)
• PCI adapter card for CoolSnap
• Computer (old G5 powerMac)

New setup:

• Hamamatsu Flash 4 LT
• Dell computer (Windows 7)
• optional USB-3 plutin card

Software:

• Micro-Manager (i.e. modified ImageJ)
• Arduino firmware (stored on the microcontroller)
• BX_Control.class (plugin to communicate with Micro-Manager)
• BX_Macros.txt (macros that communicate with BX_Control plugin)
• HamamatsuHam driver for Micro-Manager

Shutter box:
The shutter box contains the Arduino micro controller, where pin 13 controls the "hold" coil for the shutter. The state of Pin 13 is visible by the yellow on-board LED. Pin 12 controls the "fast" coil of the shutter. Additionally, pin 8 and pin 9 are programmed to operate with pull-up resistors, and are connected to the "UV-On" and "UV-off" buttons, that can be operated manually without the computer.

Installation steps for a Demo Camera and Arduino shutter:

(You need an Arduino board, but not a real camera, as "DemoCam" is a simulated substitute for a real camera)

• On the computer that operates the camera: first connect the Arduino Uno Microcontroller to the USB port that will be later used as shutter interface by Micro-Manager. Make sure that Micro-Manager and Arduino application are not open at the same time (i.e. competing for the same USB port)

• Install the Arduino software, which in turn installs the needed USB port drivers. Make sure that in menu Tools>Ports the correct Port ("Arduino Uno") is selected.

• The next step replaces any previous firmware on the Arduino micro controller board with the shutter firmware.

• Upload the firmware "MM_shutter-29-Feb.ino" onto the Arduino Uno microcontroller chip. The Upload button is the second of five icons showing a right-arrow.

• Quit the Arduino application, otherwise the USB port remains occupied.

• Load Micro-Manager

• When Micro-Manager asks to use a configuration file, choose "None"

• With the Micro-Manager window in front, go to Tools> Hardware Configuration Wizard

• Create new configuration, click Next

step 2 of 6:

• select "Demo Camera", click "Add",
• leave name= "DHub" click OK
• In "Peripheral Devices Setup", check "DCam", click OK,
• leave label = "DCam" and click OK
• Installed devices are now:
  Core
  DHub
  DCam
• From "Available Devices" choose Arduino
• leave label = Arduino-Hub
• click the "Scan" button and wait
• after max 10 seconds, "Found" appears temporarily.

• Lower part of the window should now show Port properties (RS 232 settings), such as BaudRate= 57600 etc. (If this field remains empty, the board was not recognized, e.g. if you forgot to quit the Arduino board which occupied the USB port). Leave these settings untouched and click OK.

• In "Peripheral Devices Setup", check "Digital out 8-bit" and "Shutter", then click OK

• Installed devices are now:
  Core
  DHub
  DCam
  Arduino-Hub
  Arduino-Switch
  Arduino Shutter

• click "Next"

step 3 of 6:

• leave settings and click "Next"

step 4 of 6:

• leave delay settings and click "Next"

step 5 of 6:

• Dont change any state or labels and click "Next"

step 6 of 6:

• save the configuration file

Back in the Micro-Manager Window:

• In configuration settings, add a Group by pressing the "Group +" button.
• Set Group name = "System" and check "Arduino-Switch-State", click OK.
• In the Configurations settings, the group System with Preset=0 is shown.
• Now add a Preset by selecting "System" and clicking on "Preset+". Set Preset-name to "Startup" and the preset value to "32", then click OK.
• Now overwrite the previous configuration file with the new one by going to menu Tools>Save Configuration Settings As...

Back in the Micro-Manager Window:

• make sure "Auto shutter" is checked, then take an image via "Snap": exposure of the dummy camera is simulated, and during exposure, the yellow Led on the microcontroller should be lit.

• Next time you use Micro-manager with this set-up, snapping an image with automatic shutter operation should work immediately.

Accessing the camera via macro commands:

• In order to snap pictures via macro commands, the plugin "BX_Control.class" should be present in the plugin folder of Micro-Manager.
• BX_Macros-2016.txt contains macros that can address the plugin, thus setting exposure time, operating the shutter, and snap images. The same file possibly exists with the name "StartupMacros.txt" in Micro-Manager's macro folder.

Warning: - Time delay between opening the shutter and start of exposure must still be defined (approx 150 ms time to move the shutter?)

Setup of Hamamatsu on 2-Aug-2016 with Eric van Windt:

We used the "green" DVD", that was delivered with the Flash camera

• setupLaunch
• Hokawo program

• choosing Ctrl-Alt-Delete- Task Manager to kill other tasks

• Camera Plugin
  prepares installation of all Hamamatsu cameras

• DCam + Driver
  No need to install USB module

• DCam-API Launch
  IEEE 1394
  ...
  ...
  USB camera (choose this one)

Install Shield Wizard Complete

DCAM-API (we didn't use tools yet, most important would be ExCap = exclusive capture)

Download http://sils.fnwi.uva.nl/bcb/BX_2016/