About ND Acquisition

Introduction to ND Acquisition
Common ND Experiment Options
ND Sequence Options

Introduction to ND Acquisition

NIS-Elements being a multi-purpose imaging system can be used as a handy tool to study objects, live organisms, processes, etc. The universal ND2 (N-dimensional) file format is what makes this possible. One ND2 file can contain multiple images organized according to what type of acquisition they came from. There are the following acquisition types:

Note

Each acquisition type gives a name to the corresponding dimension of the resulting ND2 file. For example, we can speak about two-dimensional TZ ND2 file, which means the file contains the Time-lapse dimension and the Z-series dimension.

Time-lapse - T

A sequence of images can be captured over a period of time and create a time-lapse image. See Time-lapse Acquisition.

Multi-point - XY

Images from different coordinates of the XY stage can be acquired. See Multi-point Acquisition.

Z-series - Z

Several techniques utilize Z-stacks of images. Such Z-stack can be for example converted to a 3D model of the specimen. See Z-series Acquisition.

Single-dimensional documents can be created automatically (using motorized accessories) or manually using commands from the Acquire menu.

Common ND Experiment Options

Custom Metadata
Executing macro commands during ND acquisition

The following options can be applied to all types of ND experiments:

Experiment

You can enter a custom name of the experiment. Also name of the phase is editable.

Path

Browse to a folder where your ND2 images will be stored.

Filename

Specifies the name of the file to be saved.

Custom Metadata

Check this option to add custom metadata to the image(s) being captured. Select the metadata set from the drop-down menu and the metadata items present in the set are automatically listed below.

For information about creating and editing custom metadata please see Custom Metadata.

Autofocus

Select the auto-focus method that best meets your needs. The Define button displays a window where you can define parameters of the selected focusing method. The focusing methods are the same as in the main menu, although their settings are independent.

Fast Automatic

Equals the method set by the Devices > Fast Auto Focus Setup command.

Steps in Range, Continuous in Range

Equal the methods set by the Devices > Auto Focus Setup command.

Close Active Shutter when idle, Close Active Shutter during Filter Change, Close Active Shutter during Stage Movement

The active shutter can be closed between single image acquisitions. Just select this option. Typically, this option is used to reduce the photo-bleaching effect on live cells.

Run Macro, Command List, Execute before each Time, Execute after each Time, Execute before Time phase, Execute after Time phase, Execute Command before Capture, Execute Command after Capture

You can define a command (or a macro) to be run in various stages of the experiment. See Executing macro commands during ND acquisition.

Load

Loads a configuration XML file. The file with the current configuration can be created using the Save button.

Save

Saves the current configuration of this dialog to an XML file. A standard Save As window appears.

Custom Metadata

To create or edit existing metadata, check the Custom Metadata checkbox in your ND experiment and click Edit. The following dialog window appears.

To create a new custom metadata set - click on New and give it a name. Click Add New and name your first metadata item. Add as many metadata items as you like and confirm their definition by clicking OK.

To edit an existing metadata set, simply change parameters of the items in the table.

You can save the whole metadata set as a .xml file by clicking Export. To import your saved metadata set, use Import. To delete the current metadata set, click Remove.

Note

The created metadata can be changed after acquisition in the image properties dialog ( File > Image Properties ).

Executing macro commands during ND acquisition

One or more macro functions can be run before or after the current phase of the experiment.

Expand the Advanced section of the experiment window.
Select the when to run the command. For example, select the Execute Command before Capture option.
Click on the drop-down menu on the right and select Command List.... This will call the Macro > Command command and display the list of all available macro functions.
Select a function from the list and confirm it by the OK button.

Note

To run a macro, use the Run macro... command from the drop-down menu and browse for the macro file saved on a disk. This way the RunMacro function will be inserted with the path to the macro file as its parameter.