there are multiple ways to do that.
The easiest one requires to have ImarisXT interface for data exchange between Matlab and Imaris:
If you have ImarisXT:
- render and export models: MIB->Menu->Models->Render model->Imaris surface…
- export the volume: MIB->Menu->File->Export image->Imaris (to have an original dataset as Volume in Imaris)
- export models as volumes to Imaris: MIB->Menu->Models->Export model to->Imaris as volume (this makes a new Volume in Imaris made of currently shown materials). The generated volume will have as many color channels as number of materials in the model.
- generate Surface in Imaris: Add New Surface button and follow the wizard for each color channel.
Note: it is possible to toggle show all or show selected material in MIB: Segmentation panel->right mouse click->Show selected material only. When a single material is shown, only that material will be exported to Imaris.
It is a bit outdated but shows the idea:
If you do not have ImarisXT you have to export materials to TIF and load TIF to Imaris, adjust the voxel size (in Z-dimension) and make surfaces. You can also save materials one-by-one to different TIF files and load them one after another to Imaris, when the “Show selected material” is checked (see above).
Let me know if something is unclear!