Particle extraction

Particle extraction is the process of using a set of positions (and possibly orientations) defined on a set of tomograms to create a set of subtomograms files. This set is represented by a data folder containing one file for each cropped subtomogram, and possibly a table retaining the metadata. Data folder and table can directly be used for subtomogram alignment

Using the catalogue

Select the tomograms in which you have models containing particles and click on the menu tab Crop particles. A new GUI will popup, with a list of models. You can then select the models that already contain crop points). Then click on Create list. This will show you an automatically created volume list file. This is just for information, no need to do anything on it. Click then on -> Crop particles, getting a GUI where you can select the sidelength in pixels, and start the actual cropping.

It will produce a data folder which will contain the cropped particles and two additional files

• a table file called crop.tbl. Column 20 assigns the particle to a particular tomogram in the volume listfile.
• a doc file with the full name of each tomogram coded by an integer in column 20 of crop.tbl

From the command line

In order to have a direct insight on how the cropping is performed, you can ignore the catalogue framework and just use the command line order dtcrop . Help on command:dtcrop

For single tomograms, all you need is table. When cropping simultaneously from different tomograms into the same data folder, there are two options:

1. Using a volume list file

   Here, the first argument of dtcrop is the name of a volume list file, the second is the code word reorder.

   In this case, the volume list file contains all the cropping information in a text file: a list of tomogram files, and a list of models or tables to be used on each tomogram

2. A table and a volume table index file

   T.B.I. In this case, the table stores explicitely the coordinates of the particles (cols 24 to 26), and in column 21 it stores an integer. The volume table index file is a text file that contains on each row an index and a tomogram file name

On each model separately

When you are manually creating a model in one of the browsers, the real workflow in an actual project involving many tomograms and modeles would be to just click the necessary points to define the user input of the model, store it in the catalogue, and move to the next model. Nevertheless, on the first model that you create with a set of parameters it is frequently useful to perform a particle extraction just to check that everything is doing what you think is doing.

If you are working in dtmview, dtmslice, Montage or any other tomogram browser connected with the model pool, you just need to select the model as the "actual" in the model pool menu tab (or right clicking on any point in the model), click on the update table points option and then on crop points on active model. This will bring you to the dtcrop GUI already pointing to the correct tomogram and to a temporary table containing the crop_points and crop_angles induces by your model.