Save separate materials

Hello,

I need some help : I haven’t understood how I could save each material separatly.
In fact, I have saved my model in .Tif file but when I open it with IMARIS, each of my materials are in the same channel.
To have each material in a separate tif file, do you have to segmente a material, save it as a model and then delete it in MIB before segmenting a new one?

Thank you in advance

Hi @Julien_B,
there are multiple ways to do that.
The easiest one requires to have ImarisXT interface for data exchange between Matlab and Imaris:
http://mib.helsinki.fi/downloads_systemreq.html#imaris

If you have ImarisXT:

Option A:

  1. render and export models: MIB->Menu->Models->Render model->Imaris surface…
  2. export the volume: MIB->Menu->File->Export image->Imaris (to have an original dataset as Volume in Imaris)

Option B:

  1. 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.
  2. 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It is a bit outdated but shows the idea: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!
Ilya

@Julien_B more specific answers:

I haven’t understood how I could save each material separatly.
To have each material in a separate tif file, do you have to segmente a material, save it as a model and then delete it in MIB before segmenting a new one?

Make sure that show selected material is checked and save to TIF:
image

I have saved my model in .Tif file but when I open it with IMARIS, each of my materials are in the same channel.

That is correct check the second video above, it shows how to make surfaces from such file

Ilya

Thank you very much, it is really clear.

I’ll try and come back to tell you how it worked

Thank you again

Best regards

It worked very fine ! thank you so much again !

Best regards

Julien