Settings in NIS-Elements

Installation of a DAQ board

Install NIS-Elements. If an NIDAQ board is needed in your setup (check the Wiring Overview chapter), select one of the following options within the Devices > National Instruments section of the installation wizard:

NI DAQ

driver for use with all I/O functions

NI PCI

legacy drivers for use with Piezo Z

See Device Manager Settings for details about settings of the NIDAQ board within NIS-Elements.

Camera Settings

No special software settings are necessary. The exposure signal is being generated on the I/O connector automatically.

Device Manager Settings

NIDAQ board

For applications using an NIDAQ board (see Wiring Overview), run the Devices > Device Manager command and Add the NIDAQ device. The following window appears:

All devices which are connected to the NIDAQ card should be added to the list of Installed devices and configured properly (see the description below). Apart from that, it is important to set the Triggering line correctly. There is a list of all NIDAQ cards found in your PC at the bottom of the window. For each card, select the PFI input connector to which the TTL triggering signal is connected.

Lambda DG-4, CoolLED pE-x, Nikon LU4A

No special settings are necessary for these devices. NIS-Elements uploads the sequence of wavelengths to the device controller via the RS232/USB interface before the triggered acquisition is started.

Agilent MLC 400 Laser Combiner
  1. Run the Devices > Device Manager command.

  2. Reveal the context menu over the NIDAQ device and click Configure....

  3. In the NIDAQ Configuration window, select Illumination Device from the right column and click Configure (add it from the left column if there is no Illumination Device).

  4. The following window appears. Select to which lines of the break-out box the camera and MLC 400 are connected.

Note

It is important that the PFI line and the output lines are attached and assigned to one NIDAQ board.

Prior NanoScanZ Piezo Stage System, Physik Instrumente E-665 Piezo controller, MCL Nano-Drive Controller
  1. Run the Devices > Device Manager command.

  2. Reveal the context menu over the NIDAQ device and click Configure....

  3. In the NIDAQ Configuration window, select Piezo Z from the right column and click Configure (add it from the left column if there is no Piezo Z).

  4. The following window appears:

Select the Analog Line to which the device is physically connected and select the Enable Triggering check box. Set mapping between voltage and position and select the type of your Piezo drive to let the system know its orientation: Stage Piezo Z or Objective Piezo Z.

Settling Time

There is always a delay between the moment the Z drive receives the signal to move and the moment it achieves the target position. By defining the Settling Time, you are telling the software to postpone the capture so images are not taken while the Z drive is moving. The actual settling time is related to travel distance:

You can optimize behavior of your piezo Z drive by setting different settling times for different travel distances. Travel distance is given as a percentage of the entire Z range.

Shutter

Custom-named shutters can be controlled by TTL or Analog signals. For this purpose, you can set-up open and close parameters, and the state of the shutter which will be set upon NIS-Elements startup or shutdown.

Acquisition Settings

Triggered Piezo Z

In either Acquire > Capture Z-Series > Capture Automatically or Applications > 4D > Define/Run ND Acquisition window, select the Triggered NIDAQ Piezo Z from the Z Device pull-down menu. Define Z stack parameters and press the Run Now button.

Multi-Excitation

Run View > Acquisition Controls > Triggered Acquisition . The following window appears:

Note

The window layout and the options-set differs depending on which Multi-Excitation Device is selected.

Common Options

Camera

Define which camera is used for acquisition. All currently connected (monochromatic) cameras are listed.

Multi-Excitation Device

Define which device is used for acquisition. All connected multi-laser illumination listed.

Setup Mode

Select the Enable Triggering option to enable the Setup Mode. Select the box and radio buttons appear in the # column. Select a channel to test its settings (live image of this channel will run).

Add New (Channel/Line)

This button adds rows to the list of channels. New channels are created at the end of the table. New Lines are inserted to the currently selected channel.

Remove (Channel/Line)

This button removes the selected row (line or a channel).

Move Up/Down

Moves the selected row up or down.

Delete All

Deletes all lines in the definition table.

# (channel number)

A check box and an automatic channel number appear in this column. Deselect the check box to omit the channel from acquisition.

Channel name

Editable channel name. It inherits the wavelength number of the inserted line by default.

Line

Select one of the available lines to be used with the channel. A line may specify a laser or other output signal (e.g. analog output).

Power

Defines power to be generated by the line. Percentage of the total power (%) for lasers or voltage of the analog output is used.

Exposure

Specify exposure time of the corresponding channel.

Enable Triggering

Select this box to turn the triggering ON. When you run the Live Image - a multichannel image shall appear on screen.

Special Options

Focus Offset

If enabled in the Advanced Settings... window, it specifies Z-offset for each channel.

Imaging

If enabled in the Advanced Settings... window, imaging and non-imaging channels can be distinguished. A non-imaging channel performs some action without capturing an image.

Use different exposures (NIDAQ HW Box required)

This option turns on/off the possibility to select different exposures for each channel. It is supported only by Andor and Photometrics Evolve 512 cameras.

Trigger signal connected to (DG4/5 only)

In most cases, the Exposure option should be turned on.

Note

Use the Readout option only when using legacy cables + Sutter DG-4.

Use shutter during readout (DG4 HW Box required)

This option is available only if HW Box and DG4 are connected. If it is selected, then the shutter is opened only during exposure and is closed during readout.

Advanced Settings... 
The following window appears when the Advanced Settings... button is pressed:

Use Focus Offset (Piezo Z)

If a piezo Z is available, this option adds a column to the channels setup. The offset value may be specified for each channel separately.

Use more lines for one channel

Enables the user to add more lines (lasers/output signals) to a single channel.

Don't sync power (allow same lines with different power)

If one line of an (analog-controlled) illumination device is used in two or more channels, its power is synchronized by default. So if you change the setting in one channel, the corresponding lines in other channels change as well. This behavior can be disabled by selecting this option.

Use non-imaging channels

Apart from capturing a channel image, the triggering signal can start other actions - for example moving a piezo Z drive. Such an action is called a non-imaging channel because the action is performed but no image is captured.

Use channel series (only dual camera/dual view)

If you check this option, the number of camera channels and excitation channels has to be the same. The first excitation channel is used with the first camera channel, the second with the second, etc.

Use these devices:

Output lines and devices which can be used during triggered acquisition are listed in this place. Select the check-boxes of the devices which should be listed in the main Triggered Acquisition window.

Multi-excitation + Triggered Piezo Z

Perform both of the above procedures and then run the acquisition.

Creating Optical Configurations for Multi-channel Triggered Acquisition

There are two ways to create an optical configuration containing a triggered-acquisition recipe.

Using the Triggered Acquisition Panel

  1. Run the View > Acquisition Controls > Triggered Acquisition command to display the panel.

  2. Select devices for triggering and define the acquisition channels (see above). Select the Enable Triggering check box.

  3. Run Calibration > New Optical Configuration and select to include Camera setting in the configuration.

Using the Optical Configurations Window

  1. Run the Calibration > Optical Configurations command.

  2. Create one optical configuration for each channel. Make sure the Camera setting and Microscope setting options are selected to ensure that settings of the camera and the triggered device are included.

    Caution

    The Enable Triggering check box in the Triggered Acquisition window must not be selected.

    Caution

    If the configurations contain also settings of devices which cannot be triggered (e.g. certain filter wheel models), the acquisition sequence will be created anyway, but the state of the filter wheel defined in the first optical configuration will be used throughout the whole sequence.

  3. Select all optical configurations which are intended to compose the triggered acquisition sequence (hold the Ctrl key).

  4. Click the Merge to TA button to create the optical configuration.

Using speed up with NIDAQ board

This special acquisition mode can accelerate all experiments within NIS-Elements using the NIDAQ board.

  1. Connect the camera exposure/fire TTL line to the NIDAQ TTL input (or analog input).

  2. Go to Devices > Device Manager and Add the NIDAQ device.

  3. The NIDAQ Configuration window opens.

  4. In the Available devices area, select Exposure Signal TTL In and click Add -->.

  5. Confirm your Configuration settings.

  6. To enable/disable the speed up function, reveal the context menu over the NIDAQ device and click Set Components... and check/uncheck the logical device.

  7. Once the speed up is enabled a notification is displayed within the ND Acquisition control panel.

Note

NIDAQ Exposure Signal TTL In should not be used with Ti-E or Ti2-E microscopes. It is designed for microscopes which cannot use the Ti recipe.