Watershed on Image Sequences

[Shreyakanakiya]

I have microCT scans of basalt rock and wish to characterize their pore geometry. For the same I have thresholded the pores. Since the pores are connected, I wish to perform watershed before calculating the circularity, surface area and volume of pores.  I tried using the 'Watershed Irregular Features' function in Biovoxxel toolbox of Fiji but it allows to perform watershed on one image at a time. Is there a way I could perform it on image sequences ?

Thanks for your time.

Regards,
Shreya

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[gankaku]

Hi Shreya,

If your images are together in a stack, the "Watershed Irregular Features"
function runs always on the complete stack.
If this is not working for you, make sure that you are running the newset
version of the BV toolbox.
All other Watershed functions like the "Adjustable Watershed" from Michael
Schmid (if I'm not wrong) do the same on stacks.

Kind regards,
Jan

2016-03-11 0:51 GMT+01:00 Shreya Kanakiya <[hidden email]>:

> I have microCT scans of basalt rock and wish to characterize their pore
> geometry. For the same I have thresholded the pores. Since the pores are
> connected, I wish to perform watershed before calculating the circularity,
> surface area and volume of pores.  I tried using the 'Watershed Irregular
> Features' function in Biovoxxel toolbox of Fiji but it allows to perform
> watershed on one image at a time. Is there a way I could perform it on
> image sequences ?
>
> Thanks for your time.
>
> Regards,
> Shreya
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Thomas Boudier-4]

Dear Shreya,

Looks you want to do a 3D watershed, I would then suggest for you to
have a look to :

http://imagej.net/Classic_Watershed

or

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

Best,

Thomas




On 11/03/2016 07:51, Shreya Kanakiya wrote:

> I have microCT scans of basalt rock and wish to characterize their pore geometry. For the same I have thresholded the pores. Since the pores are connected, I wish to perform watershed before calculating the circularity, surface area and volume of pores.  I tried using the 'Watershed Irregular Features' function in Biovoxxel toolbox of Fiji but it allows to perform watershed on one image at a time. Is there a way I could perform it on image sequences ?
>
> Thanks for your time.
>
> Regards,
> Shreya
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

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

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