Measure 3D distance of cells to a structure

Hi! I have z-stacks of confocal images that consist of 2 channels. In the first channel I have cell and in the second channel I have a structure with cells. I would like to know if there is any way to measure the distance of cells from the structure. Actually, I am wondering if there is any way to define channel 2 as a volume and afterwards measure the distance of the cells in channel 1 from that volume.

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Hi @Spyr7,

You can use the new 3D Distances plugin as part of the 3D ImageJ Suite. You will have first to segment the two channels.

The plugin will allow you to choose between center-center distances or border-border distances. You can also measure distances between only the closest objects from one channel or between all objects.

Hope this helps

Best

Thomas

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Hi @ThomasBoudier,

Thanks for the response. The plugin works fine. However, I have a question regarding the results table of 3D Distances and if the objects could be labeled on the image.

Thanks for your help

Hi @Spyr7,

Sure, what you would like to know ?

Best,

Thomas

Hi @ThomasBoudier,

I would like to know what the columns and the rows of the results table represent and if is it possible to display each object(cell) with its label on an image view.

Best,
Spyr7

Hi @Spyr7,

For the closest analysis, the results table will display :

  • label is the value of the object in the labelled image 1
  • closest_1 is the label of the closest object in image 2
  • distance_1 is the distance to this closest object
  • closest_2 is the label of the second closest object in image 2
  • distance_2 is the distance to this second closest object

Of course if you have only one image, closest object will always be itself and distance will be 0.

For the all analysis, the results table will display all the distances between all pairs of objects. Label A is the label for first image and B is the label for the second image.

Regarding the labelling of objects within the image, are you referring to putting text below the object ? For this you can use the 3DManager, just Add your image to the manager then select an image and use Label.

Hope this helps

Best,

Thomas

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Hi @ThomasBoudier,
Yes that was really intuitive. Thanks a lot!

Best,
Spyr7