IMOD

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Analyzing Tomograms Reconstructed by IMOD

Open A Tomogram from An IMOD Project

API: cylindra_builtins.imod.open_image_from_imod_project

GUI: Plugins > IMOD > Open image from an IMOD project

This function uses the .edf files in an IMOD project to open a tomogram. Tilt angles are automatically detected based on the files inside the project directory. For the meaning of each parameter, see the open_image function.

Open Multiple Tomograms from IMOD Projects

API: cylindra_builtins.imod.import_imod_projects

GUI: Plugins > IMOD > Import IMOD projects

This function imports multiple tomograms from IMOD projects using wildcard paths or list of paths, and adds them directly to the cylindra batch analyzer. You can click the "Open" button of the batch analyzer one by one to analyze each tomogram.

Create a .prm File for PEET

Single Tomogram

API: cylindra_builtins.imod.export_project

GUI: Plugins > IMOD > Export project

For subtomogram averaging and alignment, PEET uses a .prm file for the project configuration. This function refers to the STA widget and creates a .prm file according to the parameters in the widget.

Multiple Tomograms

API: cylindra_builtins.imod.export_project_batch

GUI: Plugins > IMOD > Export project as batch

Low-level Functions

Import Molecules from IMOD

API: cylindra_builtins.imod.load_molecules

GUI: Plugins > IMOD > Load molecules

This function reads molecules from files in IMOD format, which are usually used in PEET. Molecule positions are defined in a .mod file, while the molecule rotations are in a CSV file. Additionally, offsets of each molecules may be recorded in the CSV file. By passing the paths to these files, this function add molecules to the viewer.

Export Molecules for IMOD

API: cylindra_builtins.imod.save_molecules

GUI: Plugins > IMOD > Save molecules

This function saves the selected molecules as a .mod file and a CSV file in the same directory. Saved files can be directly used in PEET.

Import Lines as Splines from IMOD

API: cylindra_builtins.imod.load_splines

GUI: Plugins > IMOD > Load splines

In IMOD, you can create segmented lines with such as 3dmod viewer and save as a .mod file. The lines can be imported as splines in cylindra.

Export Splines for IMOD

API: cylindra_builtins.imod.save_splines

GUI: Plugins > IMOD > Save splines

Spline objects can be converted into segmented lines. This function saves the splines as segmented lines in a .mod file.

Warning

Reading a .mod file and saving back to a new .mod file does not preserve the original data.