Chapter 5 Documents, Archiving
5.2 ND2 Files
5.2.2 Browsing ND2 Document
When an ND2 file is opened, its structure is pictured at the bottom of the document window. There is a time line with all captured images indicated by gray markers. The blue-highlighted marker indicates the currently observed image. Below the time line, there is one row of blue rectangles for each dimension. Blue rectangles stand for single phases of each experiment dimension. In case the multichannel dimension is included, the channels are indicated by the color tabs at the very bottom of the document window.
ND Control Bar
Browse the ND document by clicking inside the time line - single time phases are highlighted by the alternating red and blue background. You can also display a frame by selecting the corresponding blue rectangle. There are other ways how to observe the ND document using the following buttons:
Chapter 5 Documents, Archiving
Insert User Event
This button inserts a marker to the current frame. User events can be pinned to any of the frames of the document in order to highlight a remarkable scene. There are number of event types. Some of them are inserted automatically (marked with*) while the ND experiment is running, others must be defined by user:
• Autofocus performed*
• Command event*
• Pause experiment*
• Resume experiment*
• Cancel experiment*
• Acquisition zero time*
• Next phase*
• Experiment paused for refocusing
• Macro event
• Event from macro
• Stimulation
• User event 1, 2, 3, 4
Once there are one or more events within the time line, you can manage them via a context menu. Right click the event marker, then a menu appears with the following options:
• Remove All Events
• Event Playing Range
• Event Manager
• Remove Event
• Edit Event
When you open the [Event Manager], all events within the ND document may be edited through the following window. The time can be put in, and the event type selected from a combo box.
Chapter 5 Documents, Archiving
User Event Selection
This button does a selection of frames of the ND file according to the [Event Playing Range] settings. Right click an event marker and pick the [Event Playing Range] command from the context menu.
A simple dialog window appears. Define the number of frames/seconds which will be selected around each event. It is specified by a single value (absolute selection size) or by the before/after values (asymmetric range).
Range Selection
Clicking this button selects a user defined range of frames. The selection is done by mouse. A range can be selected by mouse while holding the [Shift] key down. Single frames can be added/removed by mouse while holding the [Ctrl] key down similarly as when using Windows Explorer.
ND2 files may contain extremely large number of frames. It may be helpful to omit some of the frames from the selection. Right click the [Range Selection] button and a context menu appears. It enables you to select every 2nd, 5th, 10th, 20th, 50th, 100th frame. The [Select All Frames] option selects the whole range of frames as if you selected the first and the last time phase with the [Shift] key down, but preserves the [Select Every...] setting.
Disable Selection
Chapter 5 Documents, Archiving
Playing options
[Play Sequence] displays the selected/all images of the browsed dimension. [Stop Playing] stops playing the sequence at the current frame.
[Previous Position] displays the previous frame of the browsed dimension.
[Next Position] displays the next image of the browsed dimension.
[Increase Playing Speed] - the speed ranges from 0.5 FPS to 500 FPS.
[Decrease Playing Speed] - the speed ranges from 0.5 FPS to 500 FPS.
[Real Time Playing Speed] sets the playing speed to real-time (as the document was captured).
[Maximum Playing Speed for Every Frame] sets the playing speed to maximum while the display of every frame is guaranteed (when the speed is set to maximum by the + button, some frames are usually omitted when playing the sequence depending on your graphic card).
[Home Position] displays the frame of the Z dimension that was set as "home" during the acquisition.
Observing ND2 Data Sets
There are several views that can display the ND2 data sets in different ways. When you switch the view, a new document window opens. Some views are available for some dimensions only. If a view is available for two or three dimensions of the ND document, a pull-down menu appears in the top document tool bar. There you can select the dimension to be displayed.
Main View
When you open an ND2 file, it opens in this view.
Maximum/Minimum Intensity Projection View
Available for Z, T. These projections analyse all frames of one dimension and pick pixels with the maximum/minimum intensity values. These pixels are used in the resulting image.
Chapter 5 Documents, Archiving
Slices View
Available for Z, T. This view displays orthogonal XY, XZ, and YZ projections of the image sequence.
Volume View
Available for Z. This view creates a 3D model of the acquired object. Tiled View
Available for Z, T, and Multipoint. This view displays frames of the selected dimension arranged one next to other.
Chapter 5 Documents, Archiving
Chapter 5 Documents, Archiving
Synchronizer
Synchronizer enables to compare (run and view) two or more N-Dimensional documents. It automatically synchronizes view of all documents added.
To add ND documents to Synchronizer
• Open at least two ND documents you would like to observe.
• Use the [Add All] button (the first one) to add them to the synchronizer. In case there are more documents opened, use the [Add Current View] button (the second one) instead. The ND2 file being added must be active.
• The names of selected documents appear in the View Synchronizer window. To observe synchronized documents
All documents added to Synchronizer are automatically being synchronized.
• Set one of the selected documents active.
• Any action regarding the view (Z position, displayed frame, etc.) is performed on the other documents as well as on the active one.
To remove a document from View Synchronizer
• To remove one document from the synchronizer, click the check box next to its name.
Chapter 5 Documents, Archiving