count nuclei in a volume

[Cesar Mendes]

Greetings,

I want to count the number of nuclei in a tissue which express a nuclear marker (H2B:YFP). Is there a good way to do this automatically?
Attached you can see a stack of one of these images. This is a low populated example, i have other genotypes that will be much more crowded and harder to count manually.
I acquire data from a Leica confocal that can be converted to imageJ stacks.
Some cells have a decreased level of the marker and that might be an issue.
Thanks in advance!
Best,
Cesar



 
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[Thomas Boudier]

Dear Cesar,

Maybe you can have a look to the cell segmentation challenge where
similar data are available, you will get an idea of what is possible.
But basically if your signal is quite homogeneous across the tissue, you
can use thresholding, then erosion to separate touching objects. More
complex procedures may be available, like 3D band pass filtering if your
object have constant size, or iterative thresholding for dealing with
difference in intensities, contact me for details.

http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:droplet_counter:start

http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:3d_spots_segmentation:start

Best,

Thomas

On 09/12/14 03:08, Cesar Mendes wrote:

> Greetings,
>
> I want to count the number of nuclei in a tissue which express a nuclear marker (H2B:YFP). Is there a good way to do this automatically?
> Attached you can see a stack of one of these images. This is a low populated example, i have other genotypes that will be much more crowded and harder to count manually.
> I acquire data from a Leica confocal that can be converted to imageJ stacks.
> Some cells have a decreased level of the marker and that might be an issue.
> Thanks in advance!
> Best,
> Cesar
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
   /***************************************************************/
      Thomas Boudier, Associate Professor, UPMC,
      Université Pierre et Marie Curie, Paris, France.
      BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/

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

[Cesar Mendes]

Thanks Thomas and Jerome for your responses.
The Lipid Droplet Counter seems promissing. I also found a 3D Object Counter plugin that seem worth looking at (http://rsb.info.nih.gov/ij/plugins/track/objects.html).
I'm looking for someone with experience with this kind of problem that could give me a hands-on suggestion.
Thanks again,
Cesar


On Dec 8, 2014, at 10:43 PM, Thomas Boudier wrote:

> Dear Cesar,
>
> Maybe you can have a look to the cell segmentation challenge where similar data are available, you will get an idea of what is possible. But basically if your signal is quite homogeneous across the tissue, you can use thresholding, then erosion to separate touching objects. More complex procedures may be available, like 3D band pass filtering if your object have constant size, or iterative thresholding for dealing with difference in intensities, contact me for details.
>
> http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:droplet_counter:start
>
> http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:3d_spots_segmentation:start
>
> Best,
>
> Thomas
>
> On 09/12/14 03:08, Cesar Mendes wrote:
>> Greetings,
>>
>> I want to count the number of nuclei in a tissue which express a nuclear marker (H2B:YFP). Is there a good way to do this automatically?
>> Attached you can see a stack of one of these images. This is a low populated example, i have other genotypes that will be much more crowded and harder to count manually.
>> I acquire data from a Leica confocal that can be converted to imageJ stacks.
>> Some cells have a decreased level of the marker and that might be an issue.
>> Thanks in advance!
>> Best,
>> Cesar
>>
>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
>  /***************************************************************/
>     Thomas Boudier, Associate Professor, UPMC,
>     Université Pierre et Marie Curie, Paris, France.
>     BioInformatics Institute (BII)/IPAL, Singapore.
> /**************************************************************/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Thomas Boudier]

Hi,

Latest version of 3DObjectCounter can be found on the wiki site :

http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:3d_object_counter:start

an alternate version is available part of 3D ImageJ Suite :

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start

Best,

Thomas

On 10/12/14 06:57, Cesar Mendes wrote:

> Thanks Thomas and Jerome for your responses.
> The Lipid Droplet Counter seems promissing. I also found a 3D Object Counter plugin that seem worth looking at (http://rsb.info.nih.gov/ij/plugins/track/objects.html).
> I'm looking for someone with experience with this kind of problem that could give me a hands-on suggestion.
> Thanks again,
> Cesar
>
>
> On Dec 8, 2014, at 10:43 PM, Thomas Boudier wrote:
>
>> Dear Cesar,
>>
>> Maybe you can have a look to the cell segmentation challenge where similar data are available, you will get an idea of what is possible. But basically if your signal is quite homogeneous across the tissue, you can use thresholding, then erosion to separate touching objects. More complex procedures may be available, like 3D band pass filtering if your object have constant size, or iterative thresholding for dealing with difference in intensities, contact me for details.
>>
>> http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:droplet_counter:start
>>
>> http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:3d_spots_segmentation:start
>>
>> Best,
>>
>> Thomas
>>
>> On 09/12/14 03:08, Cesar Mendes wrote:
>>> Greetings,
>>>
>>> I want to count the number of nuclei in a tissue which express a nuclear marker (H2B:YFP). Is there a good way to do this automatically?
>>> Attached you can see a stack of one of these images. This is a low populated example, i have other genotypes that will be much more crowded and harder to count manually.
>>> I acquire data from a Leica confocal that can be converted to imageJ stacks.
>>> Some cells have a decreased level of the marker and that might be an issue.
>>> Thanks in advance!
>>> Best,
>>> Cesar
>>>
>>>
>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>> --
>>   /***************************************************************/
>>      Thomas Boudier, Associate Professor, UPMC,
>>      Université Pierre et Marie Curie, Paris, France.
>>      BioInformatics Institute (BII)/IPAL, Singapore.
>> /**************************************************************/
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
   /***************************************************************/
      Thomas Boudier, Associate Professor, UPMC,
      Université Pierre et Marie Curie, Paris, France.
      BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/

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