Export models to IMOD tutorial

Ilya Belevich

Models that are created in Microscopy Image Browser may be exported to IMOD for visualization. Please follow the following steps for export.

1. Open a dataset in im_browser

2. Segment the dataset

3. Export the model. The models could be exported either via the Contour or Isosurface way. If the isosurface way is used then t he objects have to be saved one by one and later combined into a single model with use of imodjoin function.
To do that:

• highlight the first material to export (Segmentation panel->Material 1)
• uncheck the Show all checkbox in the same panel
• save the material, Menu->Models->Save model as... Set Save as type as ''Countours for IMOD (*.mod)" or "Volume for IMOD (*.mrc)"; define filename and press the Save button.

4. If the ''Countours for IMOD (*.mod)" option was selected provide a density factor for points in the XY plane.

5. Start IMOD with the following command:

Countours for IMOD (*.mod)	Volume for IMOD (*.mrc)
3dmod yourfilename.mod	3dmod yourfilename.mrc
1. In the 3dmod ZaP Window you should see the contours 2. Select 3dmod Menu->Model View 3. Select 3dmod Model View->Menu->Edit->Objects->Meshing... 4. Select Surface and click the Mesh All button 5. Adjust lights with sliders in the Material section of the 3dmodv Objects window	1. In the 3dmod ZaP Window you should see the volume data 2. Select 3dmod Menu->Model View 3. Select 3dmod Model View->Menu->Edit->Isosurface... 4. Adjsut X Size, Y Size and Z size sliders to their maximal values 5. Press the Save button.