Using Segments

In contrast to point-like features (discussed in Using Points), some chromosomal features are treated as segments of chromosomes: these segments have a length dimension in addition to a position along a chromosome. A researcher might, for example, wish to know the location and length of differentially staining chromosome bands or inversion loops. The "Segment" capabilities of MicroMeasure are designed to handle situations like these.

Users may define up to 12 custom segment and/or point types, which may then be easily marked. Among applications for karyotype analysis, the ability to calculate size and location of multiple types of user-defined segments, such as C-bands, regions of asynapsis, or inversion loops, is unique to MM.

Note: while euchromatin and heterochromatin can be considered types of segments, MM handles these two special cases separately. For more information, please see Euchromatin and Heterochromatin. In some cases, at the user's discretion, it still may be advantageous to define custom segment types for eu- and heterochromatin.


Defining Segments

Since the types of segments of interest will vary from one study to another, MM allows users to define custom segment types. These may be defined prior to marking chromosomes, or may be defined as they are encountered during marking. MM handles point and segment types in similar ways. For this reason, commands for both points and segments are available on the Points menu.

Defining a custom segment type To define a new segment type, select the menu command Points | Define New Type..., then select the Segment type tab. Enter a brief descriptive name for this type: this name will be used to select this type from the Points menu. If desired, a custom color may be selected. If this option is chosen, segments of this type will be marked in a different color from the rest of the chromosome. This process may be repeated for each segment type in a project.

Marking Segments

Like all other structures, segments must be marked along chromosomes as they are encountered. It is not possible in the current version of MM to add segments after a chromosome has been traced without retracing the entire chromosome.

Segments are marked in much the same fashion as points. The only major difference is that both the start and end of each segment is must be marked. When the start of a segment is encountered, it may be marked by selecting the appropriate item from the Points menu, or by right-clicking and selecting the point type from the context menu. Marking continues as usual until the end of the segment is reached, which is then marked the same way.

The figure below illustrates how a segment is marked. Click on the Forward or Back arrows to view each step.

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Segment Possibilities and Limitations

  • Custom-defined segments may not overlap. MM will automatically mark the end of an active segment type if another segment type is initiated.
  • Centromeres and custom points may be marked while a custom segment type is active, i.e., a segment may contain a centromere or points.
  • Euchromatin and heterochromatin may be marked while a custom segment type is active, and vice versa.
  • There is a bug in the current version of MM that affects segment marking when the Chromosome | Restart Chromosome Number... command is used. Please see Known Issues for more information.

Reusing Points Lists

Since it is likely that a set of defined points and segments will be used with more than one image, MM allows users to their points lists and use them for multiple projects (MM saves the current point and segment definitions in a single file). See File | Save Points File and File | Open Points File... for more information.



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