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HomeHomeGetting Started...Getting Started...How to…How to…Imaris 8 - 'Cells' segmentation  Imaris 8 - 'Cells' segmentation
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Imaris 8 - 'Cells' segmentation
 

Hello,

I'm trying to identify and track single cells within a cell cluster using the 'Cells' segmentation (Imaris 8). I'm working with 63x magnification and my cells are stained by two colors:  mCherry for cytoplasm (RED) and yfp-mem for membrane (Yellow)

I managed  to do so by the membrane channel following this segmentation path: Cells -> detect cells only ->detect cell boundary from cell membrane -> cell body detection...

note:here i didn't use any limitation by the other channel (the cytoplasm) -  the filter type option.

Now i'm trying to do the 'Cells' segmentation by the cytoplasm channel, to check whether i get the same tracking results or not and didn't manage to get a good segmentation!

I did the following trials:

1. First i tried this segmentation path: Cells -> detect cells only ->detect cell boundary cytoplasm (using the red channel of course). Here the whole cluster was identified as on cell!

2. In addition to the previous, i used the filter type option to include the membrane channel in order to identify each and every cell in the cluster.. it didn't work

3.Tried all the above by segmenting a ROI (for an individual cell),  it didn't work as well.

Would really appreciate any suggestion.

Thank you in advance,

Nasma

 
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nasmamz wrote:

Hello,

I'm trying to identify and track single cells within a cell cluster using the 'Cells' segmentation (Imaris 8). I'm working with 63x magnification and my cells are stained by two colors:  mCherry for cytoplasm (RED) and yfp-mem for membrane (Yellow)

I managed  to do so by the membrane channel following this segmentation path: Cells -> detect cells only ->detect cell boundary from cell membrane -> cell body detection...

note:here i didn't use any limitation by the other channel (the cytoplasm) -  the filter type option.

Now i'm trying to do the 'Cells' segmentation by the cytoplasm channel, to check whether i get the same tracking results or not and didn't manage to get a good segmentation!

I did the following trials:

1. First i tried this segmentation path: Cells -> detect cells only ->detect cell boundary cytoplasm (using the red channel of course). Here the whole cluster was identified as on cell!

2. In addition to the previous, i used the filter type option to include the membrane channel in order to identify each and every cell in the cluster.. it didn't work

3.Tried all the above by segmenting a ROI (for an individual cell),  it didn't work as well.

Would really appreciate any suggestion.

Thank you in advance,

Nasma

Sun, 10 Dec 2017 13:46:39 GMT

 Hi Nasma,

please contact eusupport@bitplane.com instead.

Regards,

Daniel

 
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