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HomeHomeGetting Started...Getting Started...How to…How to…how to draw a certain image and calculate magnitude of a vector?how to draw a certain image and calculate magnitude of a vector?
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how to draw a certain image and calculate magnitude of a vector?
 
Dear all,

I have a few how questions and hoping to get some help from here to solve them.
First questions is how I can generate a certain tool and use this tool for different images?
For example, I would like to insert a circle to mark the nuclei and I would like to use the same circle for different images to the same marking of the nuclei in different images. Does anyone have any suggestion for this?

The second question is to determine the vector magnitude from two known points positions. For example, the data below is taken from IMARIS

position X   position Y    position Z   name
132.24         197.26          7167.66       A
145.38         210.46          7168.69       B

and by using X,Y,Z values of A and B and I would like to obtain the xyz values of the vector. Does anyone know how to calculate this? I am looking forward to hearing soon, thank you in advance,
 
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Hi,

>First questions is how I can generate a certain tool and use this tool for different images?
Create an XTension (in MATLAB or python), then copy it to the appropriate folder so that you can access it from inside Imaris. Details on how to write an XTension and where to place it can be found in the XT Quickstart Tutorial (open Imaris. Help -> Quickstart Tutorials -> ImarisXT).

>For example, I would like to insert a circle to mark the nuclei and I would like to use the same circle for different images to the same marking of the nuclei in different images. Does anyone have any suggestion for this?
"Circles" are not available in Imaris, but you could create spots. To mark the nuclei with spots you can use the IICells XT interface to get the nucleus positions:

tFloats2D GetNucleiCenterOfMass (int aCellIndex)

Then generate an ISpots component and create Spots at the nuclei positions (An example of how to generate and add an ISpots component can be found in the sample XTension "XT/python/XTSimpleSpotsExample.py". Note that this XTension is only available in python, not in Matlab.)

>The second question is to determine the vector magnitude from two known points positions. For example, the data below is taken from IMARIS
position X position Y position Z name
132.24 197.26 7167.66 A
145.38 210.46 7168.69 B
and by using X,Y,Z values of A and B and I would like to obtain the xyz values of the vector. Does anyone know how to calculate this?
Assuming you have an ISpots component, you can get the positions as vectors in matlab or lists in python like this:

tFloats2D GetPositionsXYZ ()

Then just subtract the corresponding positions to get the vectors from point A to point B.
 
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