Separating intracellular objects from extracellular objects

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Separating intracellular objects from extracellular objects

María Victoria Pepe
Hi

I´m studying efferocytosis of apoptotic cells by epithelial cells, for
which I´m using the *3D Objects Counter* tool. I make a map of the
apoptotic cell channel and then, I merge this map with the reslice of the
epithelial cells channel. Then I decide if the object in the map is inside
or outside the cell.  This is a slow process but generally it
works. But there are some problems when I have two objects close to each
other, one outside and one inside, because sometimes they are consider like
one only object.
How can I generate a solid mask using the reslice of the epithelial cells
channel to use it to separate intracellular objects from extracellular
objects?


I attached one image as an example.



Thanks for your time

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Re: Separating intracellular objects from extracellular objects

Krs5
Dear Maria,

Would the 3D watershed or the 3D Spot Segmentation be of use? For both see: http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:3d_spots_segmentation:start and they are part of the 3D ImageJ suite.

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility

-----Original Message-----
From: María Victoria Pepe <[hidden email]>
Sent: 20 November 2018 15:12
To: [hidden email]
Subject: Separating intracellular objects from extracellular objects

Hi

I´m studying efferocytosis of apoptotic cells by epithelial cells, for which I´m using the *3D Objects Counter* tool. I make a map of the apoptotic cell channel and then, I merge this map with the reslice of the epithelial cells channel. Then I decide if the object in the map is inside or outside the cell.  This is a slow process but generally it works. But there are some problems when I have two objects close to each other, one outside and one inside, because sometimes they are consider like one only object.
How can I generate a solid mask using the reslice of the epithelial cells channel to use it to separate intracellular objects from extracellular objects?


I attached one image as an example.



Thanks for your time

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: Separating intracellular objects from extracellular objects

María Victoria Pepe
Hi Kees!!

I´ve just downloaded the plugin, so I´ll try it soon

Thanks for your answer.

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El jue., 22 nov. 2018 a las 5:40, Straatman, Kees (Dr.) (<
[hidden email]>) escribió:

> Dear Maria,
>
> Would the 3D watershed or the 3D Spot Segmentation be of use? For both
> see:
> http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:3d_spots_segmentation:start
> and they are part of the 3D ImageJ suite.
>
> Best wishes
>
> Kees
>
>
> Dr Ir K.R. Straatman
> Senior Experimental Officer
> Advanced Imaging Facility
> Centre for Core Biotechnology Services
> University of Leicester
> www.le.ac.uk/advanced-imaging-facility
>
> -----Original Message-----
> From: María Victoria Pepe <[hidden email]>
> Sent: 20 November 2018 15:12
> To: [hidden email]
> Subject: Separating intracellular objects from extracellular objects
>
> Hi
>
> I´m studying efferocytosis of apoptotic cells by epithelial cells, for
> which I´m using the *3D Objects Counter* tool. I make a map of the
> apoptotic cell channel and then, I merge this map with the reslice of the
> epithelial cells channel. Then I decide if the object in the map is inside
> or outside the cell.  This is a slow process but generally it works. But
> there are some problems when I have two objects close to each other, one
> outside and one inside, because sometimes they are consider like one only
> object.
> How can I generate a solid mask using the reslice of the epithelial cells
> channel to use it to separate intracellular objects from extracellular
> objects?
>
>
> I attached one image as an example.
>
>
>
> Thanks for your time
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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