Scanning Module

The Scanning Module of the microscope software Morgentau M1 allows you to plan and coordinate scanning experiments graphically, and to document them automatically.

The Scanning Module embodies the scanning facilities of Morgentau M1 and allows you to conduct scanning experiments. During these experiments, scanning processes are initiated in which large numbers of so-called scanning points are subsequently approached. At each of these points a TTL-Out signal triggers, for example, a laser beam on that scanning point.

A laser can be used to stimulate selected objects. During the scanning process, researchers are then able to observe, for example, how the cells react to the laser stimulation. Instead of a laser beam, any other action can be executed by the TTL-Out signal.

Plan, execute, and document scanning experiments

The Scanning Module plans, monitors, and coordinates scanning experiments. As the Scanning Module gives you the full control over managing and conducting such experiments, the microscope software Morgentau M1 becomes a highly relevant tool to tackle entirely new research questions. Scanning experiments are a highly flexible method for today's research because they can be employed in many different research settings. A good example of an external device to be triggered by the Scanning Module is a laser, but any other external devices can, of course, also be connected.

The benefits of this module are rooted in various features that support the planning, the exectution, and the documentation of scanning experiments.

Features of the Scanning Module

The image below indicates the features of the Scanning Module:

• Control Scanning (1). Define scanning procedures based on scanning points and step protocols.
• Define Scanning Area (2). Use polygons to generate arbitrary shaped grids of scanning points.
• Order of Points (3). Order the scanning points manually, automatically, or by shuffling.
• Current Position (4). Representation of the current position of the selected motor system including the depth of the optic plane with respect to the surface of the specimen.
• Add External Devices (5). Real-time interaction with external devices by TTL-In and -Out signals.
• 2-Objective Method (6). A parafocal offset function used to combine low magnification planning images with high magnification microscope objectives.

Plan scanning experiments flexibly

In order to use scanning experiments as a powerful method to tackle different kinds of research questions, the areas that should be scanned need to be defined flexibly.

Define scanning areas and arrays of scanning points

Scanning points are drawn directly into the planning image using the polygon constructor. This feature enables the fast generation of complex scanning areas. After constructing an arbitrarily shaped polygon, this polygon can be populated by a grid of scanning points.

Order scanning points flexibly

To each scanning point, a number is assigned that indicates its rank during the scanning process. The sequential order, however, can be changed manually. A randomization of the point sequence is also possible.

Measure distances

To estimate distances within the planning image, radial distance patterns can be displayed. These radial distance patterns are also helpful when defining new scanning areas.

The two-objective mode

One key objective of the software design was to plan the scanning process on the basis of a planning image representing an arbitrarily large part of the specimen. For scanning large regions, the generation of planning images is much more convenient if one uses a low magnification objective. The two-objective mode offers the possibility to combine planning on a large scale while scanning with a high resolution. Planning images are therefore generated with a low magnification objective (e.g. a 4x-objective with an image size of about 4x3 mm), while scanning is performed using a high magnification objective, like a 60x objective and a minimum spot diameter of about 3-5 μm. This method has the advantage that only a single change of the objective lens is necessary for each slice and no additional change is necessary after the intracellular access has been established.

Execute scanning experiments validly

During the scanning process, coordinates of the scanning points are transformed into motor coordinates that determine the position at which the external device (e.g. a laser) will be triggered by the TTL-Out signal.

Monitor the current target position

The current target position of the selected motor system is represented by a red circle in the planning image and updated in real time.

Consider external signals during scanning experiments

Basically, the Scanning Module proceeds from scanning point to scanning point automatically in previously defined time intervals. However, the Scanning Module also provides the possibility, that the scanning process is only continued if a TTL-In signal is received which may be triggered by any other external device. This allows the scientist to gain enhanced control over the experiment's progress, since external signals can be considered to purposefully delay the scanning process.

Document scanning experiments automatically

The Scanning Module assists researchers with automated documentation capabilities to observe and evaluate the course of the scanning process.

Take an image at each scanning point

A question of great interest in scanning experiments is by which environment a scanning point is surrounded. A posteriori visual identification of scanning points is possible using the so-called CellSpotter function. The CellSpotter takes an image from the real-time view at each scanning point immediately before the TTL-Out signal is evoked. This additional graphical information can then be used to identify, for example, what particular cell type has been scanned. The image of each scanning point is saved as an image file, so that it can easily be deployed in research papers or presentations.

Support of two monitors

The Scanning Module supports the use of two monitors. If two monitors are used, one monitor allows monitoring the real-time scanning process with a high resolution while the second monitor displays the planning image which depicts the array of scanning points. Note that in the Professional Edition of Morgentau M1, which includes the Scanning Module, one monitor is already included. A second monitor can optionally be ordered.