Import Surfaces and Spots to Cell

Imaris Cell module provides compartmentalized quantitative information that can be useful in many applications. However, the automatic Cell detection may not work for more challenging dataset. For example, we may have to manually define the cell boundary, or edit vesicles that may not be picked up by the Cell creation wizard. To overcome these challenges, Imaris provides the option to import existing Surfaces and Spots to Cell components.

In this example, I already created the Surfaces that represent the cells and nucleus, and green and red spots that represent the vesicles within the image.

I'm going to create a new Cell object. Now, instead of going through the Creation Wizard, we can directly click ‘skip automatic creation, edit manually’. This will bring us to the Edit tab.

Click ‘Import Surface to Cell’. Surface object can be imported as Cells or Nuclei. I’m going to import first the cell Surface as Cells. Click ‘OK’.

Next, click ‘Import Spots to Vesicles’. I will first import red Spots, and give it a new name called ‘red’. Click ‘OK’.

Now, let’s go to the statistics tab. It shows that we have successfully imported one Cell, no nucleus, and 40 vesicles within the Cell. Note that the original Red Spot object actually has 41 Spots.

When importing Spots as Cell vesicles, only the Spots that are within the defined Cells would be imported. So you may see a lower vesicle count compared to the original Spot count.

Let’s go back to the Edit tab, and import additional objects. Click on ‘Import Surface to Cell’, select to import nucleus Surface, and Import as Nuclei. Click ‘OK’. We will also import green Spot object as vesicle. Notice that we have the option to either add Spots as a new type of vesicle, or we can choose to have the spots added as part of the existing vesicle type. Here I will add as new type, and give it the name ‘green’.

Now all the objects should be imported, and all statistical values will be updated automatically.