Lucia Cytogenetics

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Karyotyping of animal and plant species using LUCIA Karyo

Motivation:

The increasing demands of non-human species genetics lead us to focus on an adaptation of standard genetics image analysis methods for animals and plants. The requirements come from research laboratories as well as from routine applications in agriculture.
The work with non-human species sets high requirements on posibilities to customize software behaviour. Especially karyogram layouts, chromosome classifiers and ideograms must be simply and flexibly changed.

The species definition:

LUCIA Karyotyping enables work with different species. There are some of them predefined in the software. Our team tried to select the mostly used animal species both in reseach and routine fields. Other species can be simply added by a user.

Fig. 1
All settings regarding karyotyping and species are integrated into one form.
Fig. 2
Each species is defined by its karyotype (or typical chromosome number). The number of chromosomes can be selected as well as a sex determination scheme.

The system enables to work with the different descriptions of chromosomes. User can choose one of the standard sex determination scheme (Drosophila - XX, XY, Abraxas - WW, WZ). Optionaly simple notation can be selected using either numbers or letters.

Karyogram templates:

After the species definition other features can be set optionally. The most important is the report template. The default one is automatically generated by the system after the species definition. This one can be edited or a new one can be created. The template editor enables change of positions and alignment of each chromosome type. It is also possible to create additional positions for special purposes as markers or fragments.

Each image (in file as well as in database) stores the information about the karyogram layout. Any template can be used while editing the karyogram, the switching is immediate.

Fig. 3
The template editor enables flexibly changes of the look of karyograms.


Classifiers:

The time necessary for karyotyping can be dramatically descreased when using a properly created classifier. The LUCIA Cytogenetics system is able to classify banded chromosomes as well as homogenously stained ones. The system automatically select the classifier to be used to achive the best classification performance. In the case of banded chromosomes the banding information is used as well as chromosome lengths. When working with non-banded chromosomes the morphologic features are used (e.g. size or shape).The classifier is created in a batch process using selected images from a database.

Ideograms:

The LUCIA system is equipped with the standardly available sets of ideograms for Pig, Rat, Mouse and Cattle (and Human of course). The other sets can be created and added to the system either by our coworkers or by customers themselves. For these purposes there is an easy-to-use editor. It enables to define bands, their location and order and their properties (as density and label).

Since the ideograms hold important information about relative chromosome length and centromere position, they can be used also for other purposes than display. When there is no classifier defined for a species, the ideograms are used for classification.

Fig. 4
Karyogram editor

Fig. 5
Karyogram of a rat cell. The chromosomes were stained (G-banded) according to Levan (1974).
Fig. 6
Karyogram of a pig cell. The chromosomes have no banding.