Workflows


Measure distance of organelles from nucleus in 3D

christoph_moehl's picture
Workflow Author: 

A Great Guy

Dependencies: 
Dimension: 
3D
Comment / Instructions: 

Below as simple worklow is descibed to measure subcellular localizations relative to the nucleus.
You may e.g. quantify how far some type of vesicles or protein aggregates are apart from the nucleus border. The forflow describes a solution for 3D data.

Data requirements:

3D data, 2 channels
Channel 1: nucleus stain
Channel 2: stain for marker you want to quantify the distance to nucleus for

Workflow:

1. Nucleus detection
-Add a new SURFACE object, name it "nuclei"
-Follow the object detection wizard to segment nucleus objects

2. Marker object detection
-Add a new SURFACE object
-Follow the object detection wizard to segment nucleus objects

3. Creating of distance map channel
-In the image processing menu, go to SurfacesFunctions>>Distance Transformation
Now Matlab should start
-select nucleus objects and "distance outside objects"
A new image channel should be crated now by the Matlab script

4. Distance measurement
The generated distance map channel represents the distance from the nucleus border in pixel values. Thus, the distance of an organelle from the nucleus is equivalent to its mean gray value of the distcance map channel.
For distance measurement, just export the mean gray value of the distance channel for each object.

Please note:
In the described workflow, the distance is always calculated to the closest nucleus border. This could be also the nucleus of a neighboring cell, which generates some error. A more complex approach to avoid this error would incorporate a cell segmentation step to assign certain organelle objects to certain cells. Therefore, a cell region marker is needed.

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