Rendering of models with Imaris

(without use of ImarisXT)

Ilya Belevich

Dataset: Huh7_CmVTag1_R2_Pos5.tif (original), obtained by Serial Block Face SEM

Huh7_CmVTag1_R2_Pos5_crop.tif (cropped)

Dimensions: 32.58 x 32.58 x 2.22 μm (original)

7.01 x 4.99 x 2.22 μm (cropped)

Pixel size: 13.45 x 13.45 x 30 nm

Dataset (tif), 12 Mb
Model (mat), 0.5 Mb


1. Load the dataset. Double click on the 'Huh7_CmVTag1_R2_Pos5_crop.tif' file

2. Load the model. Segmentation Panel->Load->Model2.mat

3. Export the model as TIF files.

        I.            Select I. Select LipidDroplets in the Materials list: Segmentation Panel->Materials: LipidDroplets;

      II.            Uncheck the Show all checkbox in the Segmentation panel.

      III.            Menu->Models->Save model as...->Save as type: TIF format (*.tif); File name: LD.tif; press Save

    IV.            Repeat I - III for NuclearEnvelope, ER and Mito.

4. Start Imaris

5. Open the dataset in Imaris. Press Open and select 'Huh7_CmVTag1_R2_Pos5_crop.tif'


6. Invert the colors. Menu->Image Processing->Contrast Change->Invert...->OK


7. Set default colors.

        I.            Menu->Show Display Adjustment->ON

      II.            Display Adjustment->Click Channel 1

    III.            Click in the center of the color hex.

    IV.            Press OK

      V.            Adjust sliders in the Display adjustment window->Channel 1 for best view.





8. Set the dataset dimensions. Menu->Edit->Image Properties->Voxel Size Z: 0.030. The X/Y dimensions should be automatically detected.

9. Add models as a separate color channels.

        I.            Menu->Edit->Add Channels->select 'NE.tif'

      II.            Menu->Edit->Add Channels->select 'ER.tif'

    III.            Menu->Edit->Add Channels->select 'mito.tif'

    IV.            Menu->Edit->Add Channels->select 'LD.tif'

      V.            Set desired colors for the imported channels in the Display Adjustment window.



10. Generation of surfaces.

        I.            Turn off the Volume object: Volume Properties Panel->Surpass Scene->Uncheck Volume.

      II.            Add a model: Menu->Surpass->Surfaces

    III.            Press the blue button with a triangle (Next) in the Create Tab.


    IV.            Select the Source channel: Channel 2

      V.            Press Next.

    VI.            Adjust the left threshold value to about 0.34.


  VII.            Press Finish.

VIII.            Repeat II-VII for Channels 3-5.

11. The model is ready.