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The model is the standard way to create and store annotations in a tomogram. The most usual application of a model is in particle picking and extraction.

A model has two basic functionalities:

  1. Controls user input
    An appropriate model provides the user with tools to inspect the tomograms, locate manually or semi-automatically regions, structures or coordinates of interest and mark them.
  2. Converts the user input into particle positions
  3. Archiving the annotations.
    Models are naturally integrated inside the catalogue system, making the process of extracting particles very easy.

For the first two functionalities, Dynamooffers different types of models, adapted to the different geometries that you might encounter: filamentes, vesicles, irregularly shaped membranes, isolated particles, pseudo-crystaline arrangements....

Basic operations with models

Types of models

Isolated particles




Archiving models

After creating or working with a model, it is important to remember to save it into disk. This will save the model in an appropriate place of the catalogue folder, and also create some internal links inside the catalogue.

Importing models

Command line options

Models can read an write normally using dread and dwrite. Basic models use the extension ".omd" (object model).

Adding a model to a catalogued tomogram

A file representing a model created on a catalogued tomogram will lay in a predefined position. For instance, a model named someModel created by Dynamo in one of its catalogue-based tomogram viewers for the volume indexed as 2 in a catalogue named my Catalogue will be automatically stored in the position: myCatalogue /volume_2/models/someModel.omd

Now, if you have produced a model object myModel independently of the catalogue system, and want to embed it and assign it to a catalogued tomogram, you might have the temptation of just saving it as dwrite(myModel,'myCatalogue /volume_2/models/myModel.omd'). This is not correct, as the catalogue needs to preserve some internal links

  1. Assign the model with a Dynamo command
    dcm -c myCatalogue -l 2 -am myModel.omd
  2. Alternatively, you can tell the catalogue to relink all the files found in the models folder of one or more volumes.
    dcm -c myCatalogue --relinkAllModelFiles

If you have created a model

Plotting models